My beacons are no longer working in the newest snapshot. The beams are projected, showing that they are activated, but the effects are not applied to the player. When right clicking the beacon, I'm unable to select an effect to apply, but still get the green "Accept" check mark when placing an ingot into the box.
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Cannot confirm.
Did you create the world in 14w26c ? If you opened that world in 14w26a / 14w26b then it's broken, see MC-59294

I ran the fix a couple days ago. The only thing that wasn't fixed was the beacons. Do the beacons just need to be broken/replaced?

IDK. I deleted all my worlds touched with a/b.
Try it out.

I'll reach out to wolfiemario and see if he has a fix for it or not. Deleting the world isn't really an option at this point in time, especially if the only thing that's broken is the beacons.

Then replace the beacons.

This bug affected me while using the 14w31a snapshot. When I downgraded to the 14w30c, everything worked correctly. The beam shows but I can't get the affects to show and it won't take the cost item.

I ran into this bug with a brand new beacon and got the same results. Tried loading a new world in the most recent snapshot and the beacon still refuses to work properly. Switching to an earlier snapshot fixes the beacons. Pretty sure this is because beacons aren't identifying that the player has placed their payment in the slot. So the aura deselects and the payment remains in the slot.

Can confirm, newly placed beacon in an existing world(not loaded in any snapshot between 14w21b-14w29b) will not accept the effects chosen or take payment. Beacon still produces a beam. Other beacons that were set before still work.
Can reproduce in a new world too.

Confirmed for 14w31a. Does not affect 14w30c.
[17:42:30][17:42:30] [Server thread/ERROR]: Couldn't set beacon
io.netty.util.IllegalReferenceCountException: refCnt: 0
at io.netty.buffer.AbstractByteBuf.ensureAccessible(AbstractByteBuf.java:1173) ~[netty-all-4.0.15.Final.jar:4.0.15.Final]
at io.netty.buffer.AbstractByteBuf.checkReadableBytes(AbstractByteBuf.java:1156) ~[netty-all-4.0.15.Final.jar:4.0.15.Final]
at io.netty.buffer.AbstractByteBuf.readInt(AbstractByteBuf.java:612) ~[netty-all-4.0.15.Final.jar:4.0.15.Final]
at hb.readInt(SourceFile:639) ~[14w31a.jar:?]
at re.a(SourceFile:1049) [14w31a.jar:?]
at lz.a(SourceFile:55) [14w31a.jar:?]
at lz.a(SourceFile:8) [14w31a.jar:?]
at ie.run(SourceFile:13) [14w31a.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) [?:1.7.0_65]
at java.util.concurrent.FutureTask.run(Unknown Source) [?:1.7.0_65]
at net.minecraft.server.MinecraftServer.y(SourceFile:575) [14w31a.jar:?]
at net.minecraft.server.MinecraftServer.x(SourceFile:530) [14w31a.jar:?]
at cxc.x(SourceFile:155) [14w31a.jar:?]
at net.minecraft.server.MinecraftServer.run(SourceFile:446) [14w31a.jar:?]
at java.lang.Thread.run(Unknown Source) [?:1.7.0_65]

Still in 14w32a (world generated in 14w32a)
[16:19:28] [Server thread/ERROR]: Couldn't set beacon
io.netty.util.IllegalReferenceCountException: refCnt: 0
at io.netty.buffer.AbstractByteBuf.ensureAccessible(AbstractByteBuf.java:1173) ~[netty-all-4.0.15.Final.jar:4.0.15.Final]
at io.netty.buffer.AbstractByteBuf.checkReadableBytes(AbstractByteBuf.java:1156) ~[netty-all-4.0.15.Final.jar:4.0.15.Final]
at io.netty.buffer.AbstractByteBuf.readInt(AbstractByteBuf.java:612) ~[netty-all-4.0.15.Final.jar:4.0.15.Final]
at hb.readInt(SourceFile:639) ~[14w32a.jar:?]
at rg.a(SourceFile:1051) [14w32a.jar:?]
at ma.a(SourceFile:55) [14w32a.jar:?]
at ma.a(SourceFile:8) [14w32a.jar:?]
at ie.run(SourceFile:13) [14w32a.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) [?:1.7.0_65]
at java.util.concurrent.FutureTask.run(Unknown Source) [?:1.7.0_65]
at net.minecraft.server.MinecraftServer.y(SourceFile:575) [14w32a.jar:?]
at net.minecraft.server.MinecraftServer.x(SourceFile:530) [14w32a.jar:?]
at cxt.x(SourceFile:155) [14w32a.jar:?]
at net.minecraft.server.MinecraftServer.run(SourceFile:446) [14w32a.jar:?]
at java.lang.Thread.run(Unknown Source) [?:1.7.0_65]

Confirmed still in 14w32a (how did they miss this with the new beacon update?)

Confirmed for 14w32a. I am amazed by the fact that they missed this bug while they were working on beacon beam colours.

Confirmed for 14w32a as well. I placed four different beacons with varying sizes and fed them payment. All of them show the beam but don't accept the payment (it stays in the inventory) and I don't get any buffs.

Same issue.
[Server thread/ERROR]: Couldn't set beacon
java.lang.IndexOutOfBoundsException
at io.netty.buffer.EmptyByteBuf.readInt(EmptyByteBuf.java:470) ~[minecraft_server.jar:?]
at hb.readInt(SourceFile:639) ~[minecraft_server.jar:?]
at rg.a(SourceFile:1051) [minecraft_server.jar:?]
at ma.a(SourceFile:55) [minecraft_server.jar:?]
at ma.a(SourceFile:8) [minecraft_server.jar:?]
at ie.run(SourceFile:13) [minecraft_server.jar:?]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) [?:1.7.0_51]
at java.util.concurrent.FutureTask.run(FutureTask.java:262) [?:1.7.0_51]
at net.minecraft.server.MinecraftServer.y(SourceFile:575) [minecraft_server.jar:?]
at pl.y(SourceFile:305) [minecraft_server.jar:?]
at net.minecraft.server.MinecraftServer.x(SourceFile:530) [minecraft_server.jar:?]
at net.minecraft.server.MinecraftServer.run(SourceFile:446) [minecraft_server.jar:?]
at java.lang.Thread.run(Thread.java:744) [?:1.7.0_51]

If you leave a resource in the slot of the beacon and log out the game eats up that resource without any benefits. Although I somehow did manage to get a beacon to work once and only once. It wasn't immediate and only work when I updated to 14w32a and logged back into my test world (update is probably irrelevant). I've tried recreating this odd situation, but haven't been able to. So it seems like the actions of beacons only apply when loading up a world, but it's only by chance do you actually get the auras.

Confirmed for 14w32a. I was impressed as well that the guys didn't fix this bug when upgrading beacon stuff. I mean it doesn't make sense, right?

They were only changing the colour of the beacon light so they were unlikely to stumble across this issue. I would guess they were not aware of this bug at the time because it has only recently received above 10 votes.

I was basically spamming their twitter with this since 31a. Glad to see it's finally fixed.

This is present in 16w02a

@unknown: This is MC-95541