Phantom Chunks appearing on top of the ground level

In worlds created before 1.9 (not in a snapshot) I'm experiencing 'phantom' chunks, which appear on top of the ground level, cycling through chunks with a rate of several per second. The original blocks are still there, but they are invisible.

---- Minecraft Crash Report ----
// Ouch. That hurt :(

Time: 3-3-16 16:20
Description: Manually triggered debug crash

java.lang.Throwable
	at bcf.az(SourceFile:1694)
	at bcf.t(SourceFile:1615)
	at bcf.av(SourceFile:962)
	at bcf.a(SourceFile:392)
	at net.minecraft.client.main.Main.main(SourceFile:124)


A detailed walkthrough of the error, its code path and all known details is as follows:
---------------------------------------------------------------------------------------

-- Head --
Stacktrace:
	at bcf.az(SourceFile:1694)

-- Affected level --
Details:
	Level name: MpServer
	All players: 1 total; [bmt['mainframe98'/1160453, l='MpServer', x=-619,79, y=81,41, z=327,67]]
	Chunk stats: MultiplayerChunkCache: 441, 441
	Level seed: 0
	Level generator: ID 02 - largeBiomes, ver 0. Features enabled: false
	Level generator options: 
	Level spawn location: World: (-252,64,224), Chunk: (at 4,4,0 in -16,14; contains blocks -256,0,224 to -241,255,239), Region: (-1,0; contains chunks -32,0 to -1,31, blocks -512,0,0 to -1,255,511)
	Level time: 10423512 game time, 75199 day time
	Level dimension: 0
	Level storage version: 0x00000 - Unknown?
	Level weather: Rain time: 0 (now: false), thunder time: 0 (now: false)
	Level game mode: Game mode: creative (ID 1). Hardcore: false. Cheats: false
	Forced entities: 165 total; [xs['entity.ItemFrame.name'/1160465, l='MpServer', x=-676,50, y=67,50, z=318,03], xs['entity.ItemFrame.name'/1160464, l='MpServer', x=-677,50, y=68,50, z=299,97], xs['entity.ItemFrame.name'/1160467, l='MpServer', x=-679,97, y=68,50, z=305,50], xs['entity.ItemFrame.name'/1160466, l='MpServer', x=-674,03, y=66,50, z=307,50], xs['entity.ItemFrame.name'/1160469, l='MpServer', x=-679,97, y=67,50, z=321,50], xs['entity.ItemFrame.name'/1160468, l='MpServer', x=-675,50, y=67,50, z=308,97], xs['entity.ItemFrame.name'/1160471, l='MpServer', x=-675,50, y=67,50, z=320,97], xs['entity.ItemFrame.name'/1160470, l='MpServer', x=-678,50, y=67,50, z=322,97], xu['Painting'/1160473, l='MpServer', x=-686,50, y=66,50, z=357,97], xu['Painting'/1160472, l='MpServer', x=-681,97, y=66,50, z=346,50], xs['entity.ItemFrame.name'/1160479, l='MpServer', x=-668,50, y=68,50, z=292,03], xs['entity.ItemFrame.name'/1160478, l='MpServer', x=-661,97, y=68,50, z=186,50], xu['Painting'/1160650, l='MpServer', x=-465,00, y=67,00, z=246,03], xu['Painting'/1160458, l='MpServer', x=-723,03, y=66,50, z=346,50], xu['Painting'/1160461, l='MpServer', x=-718,50, y=66,50, z=335,03], xu['Painting'/1160463, l='MpServer', x=-690,50, y=66,50, z=357,97], xu['Painting'/1160462, l='MpServer', x=-714,50, y=66,50, z=335,03], xs['entity.ItemFrame.name'/1160497, l='MpServer', x=-641,50, y=67,50, z=294,97], xu['Painting'/1160507, l='MpServer', x=-643,50, y=66,50, z=356,97], xu['Painting'/1160505, l='MpServer', x=-652,97, y=67,50, z=366,50], xu['Painting'/1160541, l='MpServer', x=-608,00, y=67,00, z=315,03], xu['Painting'/1160506, l='MpServer', x=-641,50, y=66,50, z=356,97], vu['Bat'/1160501, l='MpServer', x=-601,47, y=63,10, z=310,51], xs['entity.ItemFrame.name'/1160503, l='MpServer', x=-641,50, y=67,50, z=305,97], xs['entity.ItemFrame.name'/1160502, l='MpServer', x=-642,50, y=67,50, z=316,97], xu['Painting'/1160544, l='MpServer', x=-608,00, y=67,00, z=304,03], xu['Painting'/1160505, l='MpServer', x=-652,97, y=67,50, z=366,50], xs['entity.ItemFrame.name'/1160504, l='MpServer', x=-641,50, y=67,50, z=327,97], xu['Painting'/1160507, l='MpServer', x=-643,50, y=66,50, z=356,97], xu['Painting'/1160540, l='MpServer', x=-608,00, y=67,00, z=293,03], xu['Painting'/1160506, l='MpServer', x=-641,50, y=66,50, z=356,97], xu['Painting'/1160509, l='MpServer', x=-635,00, y=67,00, z=238,97], xu['Painting'/1160508, l='MpServer', x=-635,00, y=67,00, z=227,97], xu['Painting'/1160518, l='MpServer', x=-635,00, y=67,00, z=329,97], xu['Painting'/1160510, l='MpServer', x=-635,00, y=67,00, z=249,97], xs['entity.ItemFrame.name'/1160481, l='MpServer', x=-662,50, y=68,50, z=336,97], xs['entity.ItemFrame.name'/1160480, l='MpServer', x=-657,03, y=68,50, z=331,50], bmt['mainframe98'/1160453, l='MpServer', x=-619,79, y=81,41, z=327,67], xu['Painting'/1160596, l='MpServer', x=-530,00, y=67,00, z=224,03], xu['Painting'/1160595, l='MpServer', x=-530,00, y=67,00, z=235,03], xs['entity.ItemFrame.name'/1160487, l='MpServer', x=-641,50, y=67,50, z=214,97], xs['entity.ItemFrame.name'/1160489, l='MpServer', x=-641,50, y=67,50, z=225,97], vx['Chicken'/1160491, l='MpServer', x=-642,49, y=62,00, z=254,78], xs['entity.ItemFrame.name'/1160490, l='MpServer', x=-641,50, y=67,50, z=236,97], xs['entity.ItemFrame.name'/1160492, l='MpServer', x=-641,50, y=67,50, z=247,97], vu['Bat'/1160495, l='MpServer', x=-603,04, y=58,99, z=311,76], xu['Painting'/1160529, l='MpServer', x=-608,00, y=67,00, z=213,03], xs['entity.ItemFrame.name'/1160531, l='MpServer', x=-601,50, y=67,50, z=237,03], xs['entity.ItemFrame.name'/1160530, l='MpServer', x=-601,50, y=67,50, z=215,03], xu['Painting'/1160533, l='MpServer', x=-608,00, y=67,00, z=224,03], xs['entity.ItemFrame.name'/1160532, l='MpServer', x=-601,50, y=67,50, z=226,03], xs['entity.ItemFrame.name'/1160535, l='MpServer', x=-601,50, y=67,50, z=248,03], xu['Painting'/1160534, l='MpServer', x=-608,00, y=67,00, z=235,03], xu['Painting'/1160536, l='MpServer', x=-608,00, y=67,00, z=246,03], xs['entity.ItemFrame.name'/1160539, l='MpServer', x=-601,50, y=67,50, z=295,03], xu['Painting'/1160541, l='MpServer', x=-608,00, y=67,00, z=315,03], xu['Painting'/1160540, l='MpServer', x=-608,00, y=67,00, z=293,03], xs['entity.ItemFrame.name'/1160543, l='MpServer', x=-601,50, y=67,50, z=317,03], xs['entity.ItemFrame.name'/1160542, l='MpServer', x=-601,50, y=67,50, z=306,03], xu['Painting'/1160513, l='MpServer', x=-635,00, y=67,00, z=318,97], yd['item.item.dyePowder.black'/1286467, l='MpServer', x=-637,71, y=46,00, z=335,88], xu['Painting'/1160513, l='MpServer', x=-635,00, y=67,00, z=318,97], vu['Bat'/1160512, l='MpServer', x=-627,50, y=60,14, z=293,61], xu['Painting'/1160514, l='MpServer', x=-635,00, y=67,00, z=307,97], xu['Painting'/1160514, l='MpServer', x=-635,00, y=67,00, z=307,97], yd['item.item.dyePowder.black'/1160517, l='MpServer', x=-637,30, y=45,00, z=334,06], xu['Painting'/1160519, l='MpServer', x=-634,97, y=66,50, z=422,50], xu['Painting'/1160518, l='MpServer', x=-635,00, y=67,00, z=329,97], xu['Painting'/1160521, l='MpServer', x=-630,50, y=66,50, z=463,97], xu['Painting'/1160520, l='MpServer', x=-634,97, y=66,50, z=424,50], vu['Bat'/1160523, l='MpServer', x=-615,25, y=52,10, z=398,56], xu['Painting'/1160525, l='MpServer', x=-619,03, y=66,50, z=468,50], xs['entity.ItemFrame.name'/1160561, l='MpServer', x=-563,50, y=67,50, z=294,97], xu['Painting'/1160649, l='MpServer', x=-465,00, y=67,00, z=224,03], xs['entity.ItemFrame.name'/1160563, l='MpServer', x=-563,50, y=67,50, z=316,97], xs['entity.ItemFrame.name'/1160562, l='MpServer', x=-563,50, y=67,50, z=305,97], xu['Painting'/1160648, l='MpServer', x=-465,00, y=67,00, z=235,03], xu['Painting'/1160565, l='MpServer', x=-560,03, y=67,50, z=343,50], xu['Painting'/1160564, l='MpServer', x=-560,03, y=67,50, z=337,50], xs['entity.ItemFrame.name'/1160566, l='MpServer', x=-565,97, y=67,50, z=340,50], xu['Painting'/1160565, l='MpServer', x=-560,03, y=67,50, z=343,50], xu['Painting'/1160521, l='MpServer', x=-630,50, y=66,50, z=463,97], xu['Painting'/1160564, l='MpServer', x=-560,03, y=67,50, z=337,50], xu['Painting'/1160575, l='MpServer', x=-557,00, y=67,00, z=227,97], xu['Painting'/1160544, l='MpServer', x=-608,00, y=67,00, z=304,03], xu['Painting'/1160525, l='MpServer', x=-619,03, y=66,50, z=468,50], xu['Painting'/1160594, l='MpServer', x=-530,00, y=67,00, z=213,03], yd['item.item.dyePowder.black'/1160550, l='MpServer', x=-586,47, y=47,50, z=304,89], yd['item.item.dyePowder.black'/1160552, l='MpServer', x=-587,82, y=48,00, z=305,50], xs['entity.ItemFrame.name'/1160557, l='MpServer', x=-563,50, y=67,50, z=225,97], xs['entity.ItemFrame.name'/1160556, l='MpServer', x=-563,50, y=67,50, z=214,97], xs['entity.ItemFrame.name'/1160559, l='MpServer', x=-563,50, y=67,50, z=247,97], xs['entity.ItemFrame.name'/1160558, l='MpServer', x=-563,50, y=67,50, z=236,97], xu['Painting'/1160510, l='MpServer', x=-635,00, y=67,00, z=249,97], xu['Painting'/1160595, l='MpServer', x=-530,00, y=67,00, z=235,03], xu['Painting'/1160536, l='MpServer', x=-608,00, y=67,00, z=246,03], xu['Painting'/1160594, l='MpServer', x=-530,00, y=67,00, z=213,03], xu['Painting'/1160597, l='MpServer', x=-530,00, y=67,00, z=246,03], xu['Painting'/1160596, l='MpServer', x=-530,00, y=67,00, z=224,03], xu['Painting'/1160599, l='MpServer', x=-529,00, y=67,00, z=296,03], xu['Painting'/1160601, l='MpServer', x=-530,00, y=67,00, z=315,03], xu['Painting'/1160600, l='MpServer', x=-530,00, y=67,00, z=304,03], xu['Painting'/1160602, l='MpServer', x=-529,03, y=67,00, z=329,00], xu['Painting'/1160581, l='MpServer', x=-557,00, y=67,00, z=307,97], xu['Painting'/1160577, l='MpServer', x=-557,00, y=67,00, z=249,97], xu['Painting'/1160576, l='MpServer', x=-557,00, y=67,00, z=238,97], xu['Painting'/1160582, l='MpServer', x=-557,00, y=67,00, z=318,97], xu['Painting'/1160581, l='MpServer', x=-557,00, y=67,00, z=307,97], xu['Painting'/1160584, l='MpServer', x=-559,97, y=72,00, z=337,00], xu['Painting'/1160580, l='MpServer', x=-557,00, y=67,00, z=296,97], xs['entity.ItemFrame.name'/1160583, l='MpServer', x=-558,97, y=67,50, z=343,50], xu['Painting'/1160582, l='MpServer', x=-557,00, y=67,00, z=318,97], xu['Painting'/1160584, l='MpServer', x=-559,97, y=72,00, z=337,00], xu['Painting'/1160602, l='MpServer', x=-529,03, y=67,00, z=329,00], xu['Painting'/1160580, l='MpServer', x=-557,00, y=67,00, z=296,97], xu['Painting'/1160600, l='MpServer', x=-530,00, y=67,00, z=304,03], xu['Painting'/1160601, l='MpServer', x=-530,00, y=67,00, z=315,03], xu['Painting'/1160599, l='MpServer', x=-529,00, y=67,00, z=296,03], xs['entity.ItemFrame.name'/1160625, l='MpServer', x=-498,50, y=67,50, z=225,97], xs['entity.ItemFrame.name'/1160624, l='MpServer', x=-498,50, y=67,50, z=214,97], xs['entity.ItemFrame.name'/1160627, l='MpServer', x=-498,50, y=67,50, z=247,97], xs['entity.ItemFrame.name'/1160626, l='MpServer', x=-499,50, y=67,50, z=236,97], xu['Painting'/1160637, l='MpServer', x=-492,00, y=67,00, z=249,97], vu['Bat'/1259190, l='MpServer', x=-553,18, y=56,60, z=358,92], vu['Bat'/1259189, l='MpServer', x=-562,83, y=49,80, z=307,30], xu['Painting'/1160647, l='MpServer', x=-465,00, y=67,00, z=213,03], xu['Painting'/1160635, l='MpServer', x=-492,00, y=67,00, z=227,97], vu['Bat'/1259193, l='MpServer', x=-542,36, y=55,63, z=334,35], xu['Painting'/1160637, l='MpServer', x=-492,00, y=67,00, z=249,97], xu['Painting'/1160636, l='MpServer', x=-492,00, y=67,00, z=238,97], xs['entity.ItemFrame.name'/1160613, l='MpServer', x=-523,50, y=67,50, z=226,03], xs['entity.ItemFrame.name'/1160612, l='MpServer', x=-523,50, y=67,50, z=215,03], xs['entity.ItemFrame.name'/1160615, l='MpServer', x=-523,50, y=67,50, z=248,03], yd['item.item.dyePowder.black'/1169831, l='MpServer', x=-645,41, y=45,00, z=317,19], xs['entity.ItemFrame.name'/1160614, l='MpServer', x=-523,50, y=67,50, z=237,03], xs['entity.ItemFrame.name'/1160617, l='MpServer', x=-525,50, y=67,50, z=306,03], xs['entity.ItemFrame.name'/1160616, l='MpServer', x=-525,50, y=67,50, z=293,03], xs['entity.ItemFrame.name'/1160619, l='MpServer', x=-525,50, y=67,50, z=323,03], xs['entity.ItemFrame.name'/1160618, l='MpServer', x=-523,50, y=67,50, z=321,97], xu['Painting'/1160636, l='MpServer', x=-492,00, y=67,00, z=238,97], xu['Painting'/1160533, l='MpServer', x=-608,00, y=67,00, z=224,03], xu['Painting'/1160577, l='MpServer', x=-557,00, y=67,00, z=249,97], yd['item.item.dyePowder.black'/1197274, l='MpServer', x=-587,03, y=47,50, z=302,10], xu['Painting'/1160534, l='MpServer', x=-608,00, y=67,00, z=235,03], xu['Painting'/1160508, l='MpServer', x=-635,00, y=67,00, z=227,97], xu['Painting'/1160509, l='MpServer', x=-635,00, y=67,00, z=238,97], xu['Painting'/1160575, l='MpServer', x=-557,00, y=67,00, z=227,97], xu['Painting'/1160458, l='MpServer', x=-723,03, y=66,50, z=346,50], xu['Painting'/1160597, l='MpServer', x=-530,00, y=67,00, z=246,03], vu['Bat'/1259201, l='MpServer', x=-646,25, y=36,10, z=310,25], xu['Painting'/1160635, l='MpServer', x=-492,00, y=67,00, z=227,97], xu['Painting'/1160472, l='MpServer', x=-681,97, y=66,50, z=346,50], xu['Painting'/1160473, l='MpServer', x=-686,50, y=66,50, z=357,97], vu['Bat'/1299965, l='MpServer', x=-544,17, y=59,15, z=276,41], xu['Painting'/1160519, l='MpServer', x=-634,97, y=66,50, z=422,50], xu['Painting'/1160576, l='MpServer', x=-557,00, y=67,00, z=238,97], xu['Painting'/1160462, l='MpServer', x=-714,50, y=66,50, z=335,03], xu['Painting'/1160529, l='MpServer', x=-608,00, y=67,00, z=213,03], xu['Painting'/1160461, l='MpServer', x=-718,50, y=66,50, z=335,03], xu['Painting'/1160520, l='MpServer', x=-634,97, y=66,50, z=424,50], xu['Painting'/1160463, l='MpServer', x=-690,50, y=66,50, z=357,97], vu['Bat'/1305067, l='MpServer', x=-586,48, y=55,52, z=332,25], vu['Bat'/1305065, l='MpServer', x=-564,98, y=53,58, z=313,71], vu['Bat'/1305069, l='MpServer', x=-558,67, y=53,80, z=306,67], vu['Bat'/1305068, l='MpServer', x=-594,10, y=58,87, z=338,55]]
	Retry entities: 0 total; []
	Server brand: vanilla
	Server type: Integrated singleplayer server
Stacktrace:
	at bku.a(SourceFile:365)
	at bcf.b(SourceFile:2515)
	at bcf.a(SourceFile:401)
	at net.minecraft.client.main.Main.main(SourceFile:124)

-- System Details --
Details:
	Minecraft Version: 1.9
	Operating System: Windows 10 (amd64) version 10.0
	Java Version: 1.8.0_25, Oracle Corporation
	Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Oracle Corporation
	Memory: 154817928 bytes (147 MB) / 443973632 bytes (423 MB) up to 1060372480 bytes (1011 MB)
	JVM Flags: 6 total; -XX:HeapDumpPath=MojangTricksIntelDriversForPerformance_javaw.exe_minecraft.exe.heapdump -Xmx1G -XX:+UseConcMarkSweepGC -XX:+CMSIncrementalMode -XX:-UseAdaptiveSizePolicy -Xmn128M
	IntCache: cache: 0, tcache: 0, allocated: 13, tallocated: 99
	Launched Version: 1.9
	LWJGL: 2.9.4
	OpenGL: ATI Radeon HD 4800 Series GL version 3.3.11672 Compatibility Profile Context, ATI Technologies Inc.
	GL Caps: Using GL 1.3 multitexturing.
Using GL 1.3 texture combiners.
Using framebuffer objects because OpenGL 3.0 is supported and separate blending is supported.
Shaders are available because OpenGL 2.1 is supported.
VBOs are available because OpenGL 1.5 is supported.

	Using VBOs: No
	Is Modded: Probably not. Jar signature remains and client brand is untouched.
	Type: Client (map_client.txt)
	Resource Packs: 
	Current Language: English (US)
	Profiler Position: N/A (disabled)
	CPU: 4x Intel(R) Core(TM)2 Quad CPU Q8300 @ 2.50GHz