If you leave the immediate area of the cart crash and then return a few times to get that series of cutscenes over, does that make a difference?
Do you have previous recent saves with this character, that you could revert to, or perhaps narrow down when the problem occurred?
You could try using
iZakaroN's SaveEditor (or from
Kiya's site, with description) to unlearn all your skills, load the game and then re-learn them. First test with a spell you have not tried yet.
Check your PM (click '
My Home' in the top menu bar, then 'Received Private Messages').