I had it happen once and I had no clue. But it hasn't happened to me since. I did lesson their class schedule so they could really focus on their studies and participate in school activities. I can't do 4 classes. It's way too stressful to get all the homework done and all the term papers edited, etc. I do 3 and that's way easier. 2 was good because then Sim can do really well but that got too boring because then my Sim had nothing to do. I don't have my Sim maxed out in any skill level. University helps you advance in careers so you don't start out at the bottom. I have my Sim build her skill levels by taking the skill classes they provide for the courses she's taking. That seemed to help too but sounds like you already did that part. I have no idea why my Sim was put on probation that one time, but I think I accidentally cheated on something so that could have been it too and I think it was when she was maxed out on classes and she didn't have time to concentrate on every thing needed. I also think organizing the board before you turn it in is a good idea and to have you Sim practice a little too. Not totally sure if that helps but practice does make perfect so I'm sure it works somehow to their advantage. This is all just insight of playing and trying to figure out the right course work for me to handle and making my Sim happy in the mean time.
Edit: I do have my Sims take notes for like the first two classes and then actively listen the rest of the time. The taking notes just gains skill level and seems to make them happier (not physically but grade wise) about attending class and I believe it goes towards you grade. It's either that or the actively listen one that does it, I can't remember.
