Saw this thread and I'm not certain the original problem was addressed. I ran into the same issue and after a lot of troubleshooting (and help from TT customer service) found out that the 1099-Q must be fully entered before the 1098-T. There's no logical reason why, but fixing the order of entry worked for me.
Here are two threads on the issue:
Why 1099-Q form increased my tax?
Tip when entering 1098-T with a corresponding 1099-Q
