Unique server bug I don't think has been solved

My server was working perfectly fine until a little while ago, when it got this error:

[21:36:38 INFO]: Starting minecraft server version 1.8.8
[21:36:38 ERROR]: Exception handling console input
java.io.IOException: The handle is invalid
at java.io.FileInputStream.readBytes(Native Method) ~[?:1.8.0_45]
at java.io.FileInputStream.read(FileInputStream.java:255) ~[?:1.8.0_45]
at java.io.BufferedInputStream.read1(BufferedInputStream.java:284) ~[?:1.8.0_45]
at java.io.BufferedInputStream.read(BufferedInputStream.java:345) ~[?:1.8.0_45]
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) ~[?:1.8.0_45]
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) ~[?:1.8.0_45]
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) ~[?:1.8.0_45]
at java.io.InputStreamReader.read(InputStreamReader.java:184) ~[?:1.8.0_45]
at java.io.BufferedReader.fill(BufferedReader.java:161) ~[?:1.8.0_45]
at java.io.BufferedReader.readLine(BufferedReader.java:324) ~[?:1.8.0_45]
at java.io.BufferedReader.readLine(BufferedReader.java:389) ~[?:1.8.0_45]
at ko$2.run(SourceFile:81) [minecraft_server.1.8.8.jar:?]
[21:36:38 INFO]: Loading properties
[21:36:38 INFO]: Default game type: SURVIVAL
[21:36:38 INFO]: Generating keypair
[21:36:38 INFO]: Starting Minecraft server on *:25565
[21:36:38 INFO]: Using default channel type
[21:36:39 INFO]: Preparing level "Survival Multiplayer"
[21:36:40 INFO]: Preparing start region for level 0
[21:36:41 INFO]: Preparing spawn area: 38%
[21:36:42 INFO]: Preparing spawn area: 84%
[21:36:42 INFO]: Done (3.268s)! For help, type "help" or "?"

I have not seen anything like this error, because the last line is different from anything else, "at ko$2.run(SourceFile:81)[minecraft_server.1.8.8.jar:?]". This is a serious problem; I only get around 10 results of the problem, and none of them have been solved. I have tried installing and uninstalling different java versions, trying to use another server, switching internets, messing with the server.properties to see if anything solves the problem, and even reinstalling Minecraft, but nothing I do will work. Can someone help solve my problem?