I actually feel rather stupid for posting so quickly. I have been so spoiled with my crash/issue free OS X that I forgot about the basics. I used to have to zap the PRAM at least weekly 4 or so years ago on OS 9 and earlier. I will admit it when I pull a stupid move. The fix - restart. Duh. What is this your first gig? My bad.
Have you zapped the PRAM on OS X? Does it still mess up preferences for other programs as it did in 9?