@Theraze I consider you an advanced user so please don't consider the below suggestions as patronising, just trying to rule a few things out.
Seems to be hard to track down, any objections to sending me your pref files so I can diff them with mine? long shot I know, but might help?
Also: what is your Java version and OS version.
Are you running kolmafia from a priveliged location (root of system drive, windows, system(32) folder, program files?
Have you tried: copy your .jar to a new directory and let it create all new folders and settings, add your settings, scripts and ccs back in as you need them. I know this is a pain in the ass but it may track down the problem. if a 'clean' install of kolmafia has the problem then I think we have to consider it as a java or system problem..