I had the SAME EXACT PROBLEM! I reinstalled thought and it fixed it. I cant imagine what is happeneing. There are a few things to try:
1: re install JK to a NEW directory
2: If 1 dosnt work try uninstalling JK, then search your registry for ALL things that have to do with JK and delete them
(I am not 100% sure of the effects of this one but I had no problems with it) after that, re-install JK
3: I hate to say this but if neither of my ideas work you may have to contact LucasArts tech support. If you call the 800 number you may get a faster response.