It shouldn't have anything to do with it, but these are the .vbs and .bat files I use to run mafia (and a few other programs):
Set oShell = CreateObject ("Wscript.Shell")
strArgs = "Programs\KoLmafia\KoLmafia.bat"
oShell.Run strArgs, 0, true
This allows me to run mafia on any Windows 7 or 8 system without having to be constantly conscious of what drive letter. It automatically finds and assigns the appropriate directory structure, keeping it relative to where the .jar itself is located. I scanned my settings and none of them contained any drive reference.
..\..\jdk\bin\javaw.exe -jar KoLmafia.jar
For reference, I also have Eclipse, Notepad++, and Minecraft running off it as well.
I'm almost willing to write it off as a glitch caused by an SVN miscommunication. I just wanted to see if my thinking was right though. I was thinking something was causing it to access the SVN root rather than the appropriate directory.