I have a standard hand-rolled Nimble Human Fist/5th level Burglar that I'm using for testing. Here are the issues I've discovered so far:
Character has Mod.Leather Armor with Discreet, Light and Fitted. Armor Check Penalty is not being reduced for Fitted.
Windows 8 x64, Java 1.7, PCGen 6.1.04
hp Pavilion g6