I know a may be a few builds behind but shouldn't be getting this right?
http://hastebin.com/huxijomaqa.avrasm

I would highly recommend trying the latest developer build. See #646 for more info.

Ah okay. We did just move our servers over to a HDD due to storage issues, and all our databases are still on the SSD

Side note: you wouldn't happen to know of any ways to split the debug messages from the rest on the normal console out? We are using log4j, but I haven't found anything on it yet

You can use grep if you're on linux, or you can use a custom log4j config with custom pattern matching, e.g. http://stackoverflow.com/a/731106 requires starting up the server with the following flag -Dlog4j.configurationFile=LocationOfYourConfigFileHere