I have this same problem. The instructions do not give me any of this. The distribution code on the deductible (traditional) IRA is 7 and that might be what's causing the problem. I did not get any kind of tax form for my Roth IRA.
My situation: I just did a rollover of some (not all of) already existing funds from a traditional IRA to the Roth. I imported the 1099-R form from the source (traditional) IRA. So like you, I'm getting that excess contribution problem and like you, TurboTax is making me pay taxes that I shouldn't have to.
