Just in case anybody besides me is still playing The Sims 2 and encounters this problem...
When I sent a batch of Sims to college, one of the six had a small performance bar despite having all three necessary skills.
I tried a few things that didn't work, and then I went to Google. The consensus was that this is merely a display issue; if you do all the right things (have your Sim build skills, write his term paper, go to class, etc.) then your Sim will still pass the semester even though his performance meter won't reflect his passing grade.
So I just had my poor Sim study his little brains out (he's a Knowledge Sim, so he wasn't too unhappy with that) and sent him to finals with much fear and trembling. Lo and behold, he got a 4.0.
Later, I moved him from the dorm to a Greek house. His performance meter has been displaying normally ever since. So, if you're having this problem and can't stand seeing that red bar even when you know it's not accurate, try moving your Sim to a different lot and seeing if that makes it better.