Is it possible that they were spells that your PC was not, level-wise, supposed to be able to get? This can cause problems, because the game has checks for such things, it references back and forth through scripted variables and their corresponding .2da... so if you aren't supposed to have a Force Power at the level you are, yet you DO have that power, the game might just freak out on you.
Same thing for Prestige class powers, if there are any ( :?: )
That's my only idea, but it seems to jive with my own memory of a similar experience.