http://hastebin.com/okamejeyet.vhdl

We use AutoSaveWorld to auto-save and auto-backup at intervals. Any ideas if this would be Playervaults issue, or AutoSaveWorld's?

This issue seemed to have just started happening recently, like a week and a half ago. And i'm commonly seeing this when it's backuping as well:
http://hastebin.com/oxoguqufuh.avrasm

We re-enabled backuping, and on the first backup server crashed.

Full server log file: https://www.dropbox.com/s/3p5filwd69jd506/server-2015-09-15-19-21-34-crashed.log?dl=0

Autobackup begins at line 3612 (if viewing with notepadplusplus).

I believe this issue started happening after updating to one of your August builds.

Edit: An interesting thing I've noticed is that the auto-backup feature is crashing 2 out of the 3 servers with it enabled. Not sure why it isn't crashing our Creative server.

Increase open files limit, i'm not sure why randomaccess files are not closed properly, will have to figure it out later.

What java version do you have?

Okay, i reverted to use FileInputStream, but that was a blind commit, so you should also check if backup is done properly.

java version "1.8.0_31"
Java(TM) SE Runtime Environment (build 1.8.0_31-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)

Update to latest dev build version, or increase the limit of maximum open files (ulimit)

Yep. Maybe for some reason RandomAccessFile channel input stream doesn't close properly, i will check this later.

We have been on the latest dev build. (861).

So is the only option increasing the limit of maximum open files?

Anyway try latest dev build, maybe it will solve your problem without changing the limit of open files.