First, if you rolled the money directly from the pension fund to the IRA, there should be no penalties.
I'm not totally familiar with how TT asks the questions, but, for each 1099-R, there is a series of questions. One of which should be asking what you did with the money.
Box 7 of the 1099R should have an entry. If this was a direct rollover, Box 7 should have G selected, direct rollover. That should come up when you enter the information from the 1099R into TT.
That should eliminate TT asking about or inferring ongoing penalties until you repay it.
Hopefully that solves your problem.
**Disclaimer: Effort has been made to offer correct information; but due to the discussion forum limitations, the poster disclaims any legal responsibility for the accuracy of the poster's response**
