1.7.8 Server Not Connectable

When I updated my server from 1.7.5 to 1.7.7 the server started normally then the mb started to go up to 400 and 500. I didn't know what to do and I checked the online-mode/offline-mode before starting it for the first time. Then when 1.7.8 came out I updated again but everytime when I check the server log it says the following:

[10:42:43] [Server thread/INFO]: Starting minecraft server version 1.7.8
[10:42:43] [Server console handler/ERROR]: Exception handling console input
java.io.IOException: The handle is invalid
	at java.io.FileInputStream.readBytes(Native Method) ~[?:1.7.0_51]
	at java.io.FileInputStream.read(Unknown Source) ~[?:1.7.0_51]
	at java.io.BufferedInputStream.read1(Unknown Source) ~[?:1.7.0_51]
	at java.io.BufferedInputStream.read(Unknown Source) ~[?:1.7.0_51]
	at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) ~[?:1.7.0_51]
	at sun.nio.cs.StreamDecoder.implRead(Unknown Source) ~[?:1.7.0_51]
	at sun.nio.cs.StreamDecoder.read(Unknown Source) ~[?:1.7.0_51]
	at java.io.InputStreamReader.read(Unknown Source) ~[?:1.7.0_51]
	at java.io.BufferedReader.fill(Unknown Source) ~[?:1.7.0_51]
	at java.io.BufferedReader.readLine(Unknown Source) ~[?:1.7.0_51]
	at java.io.BufferedReader.readLine(Unknown Source) ~[?:1.7.0_51]
	at lu.run(SourceFile:81) [minecraft_server.1.7.8.exe:?]
[10:42:43] [Server thread/INFO]: Loading properties
[10:42:43] [Server thread/INFO]: Default game type: SURVIVAL
[10:42:43] [Server thread/INFO]: Generating keypair
[10:42:45] [Server thread/INFO]: Starting Minecraft server on *:25565
[10:42:46] [Server thread/INFO]: Preparing level "Stardustcraft"
[10:42:46] [Server thread/INFO]: Preparing start region for level 0
[10:42:48] [Server thread/INFO]: Preparing spawn area: 0%
[10:42:49] [Server thread/INFO]: Preparing spawn area: 13%
[10:42:53] [Server thread/INFO]: Preparing spawn area: 26%
[10:43:05] [Server thread/WARN]: Wrong location! wn['Pig'/189, l='Stardustcraft', x=-47.14, y=64.00, z=161.72] (at -3, 10 instead of -4, 10)

I don't know if I'm missing a certain kind of java or its the files in my server. I run a vanilla 1.7.8 server and the average tick is 0.000 ms and after two hours its something like average tick: 900000000 ms and when I try joining it says something like Internal Exception: io.netty.handler.timeout.ReadTimeoutException

The it has an X over the connection bars and it says old in red and I'm playing in the right version.