Problem solved.
I had gone back in to After Effects and changed the AE comp to 29.97, exported, then brought the new file in to Premiere. What I didn’t realize is that when the student created the original sequences in Premiere, the sequences changed from 29.97 to 25 fps PAL to match the AE video output.
So, I was bringing in 29.97 video into 25 fps sequences. Once I realized that, I just created new sequences for 29.97 and pulled in the 29.97 video and now all is well. The odd thing is, there were some 24 fps sequences and some 23.9xx sequences, but those worked fine.
Of course, I didn’t realize the solution until after I had made a bD disc for every senior,