A mi tambien me pasa lo mismo, pero al 1 he jugado desde dvd y hd y nunca tuve problema la verdad.
Edit: he encontrado esto por ahi:
Actually, you might try changing a value in the swkotor2.ini
[Game Options]
AutoPause_LeaderKilled=0
AutoPause_EnemySighted=1
AutoPause_UseVertMenu=0
AutoPause_UseHorzMenu=0
AutoPause_RoundMode=0
AutoLevelUpNPCs=0
EnableTutorialWindows=0
UseLocalContent=1 << (This is usually set to 0)
After making this change, I started 10 new games and played them up to the point where T3 gets zapped... not one of them glitched. Haven't seen another glitch anywhere since. I don't know if that really made a difference, but it's worth a try.
I've also been using an override folder with quite a few modded files and still no problems.