Yeah, KOTOR isn't known for being a bug-free game, that's for sure! Are you playing the XBox version or the PC version? You could take your save to another XBox or PC and play it there (if you had the resources or friends).
I read in a guide that every player was supposed to destroy the chambers when fighting Malak at the end. Of course, I just let him regenerate his health all million times and the fight lasted forever. I never tried attacking the chambers, but I did read that you can do it on both sides. That guide may have been wrong though! Sounds like you need to find a way to get rid of that chamber before he gets there. If you can't find a way, check out
www.gamefaqs.com . Good luck!
-Lasereth