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:
PCGen calculates number of Interests as 3 where it should be 5 (home language, homeland study + 2 others + 1 @ 2nd level).
Windows 8 x64, Java 1.7, PCGen 6.1.04
hp Pavilion g6