Hmmm... not sure if the Bastila on Korriban would be the cause, although I think it does alter the partytable... been a while.
The problem you describe seems vaguely familiar to me, and it seems that when I was having this issue, the problem was ultimately something to do with my wireless desktop!
If you are using a wireless setup, try that section with a plugged in mouse/board. Just for the heck of it... IIRC, I did that, gameplay resumed normally, then I saved and went back to wireless and was fine. When I had the gameplay symptons you describe, it was intermittent and not related solely to the Korriban academy, so this is a longshot at best.
Just out of curiosity, you have patched your game?