I am having the same issue. I converted $45,000 from a Traditional IRA to a Roth IRA. I expected to pay the taxes, but Turbo Tax is telling me that I owe 6% on the excess over the annual contribution limit of $6,000, which is $39,000, thus the penalty I have to pay is $2,340. This is not a contribution, but rather a conversion. Why does Turbo Tax continue to say I owe the penalty? I don't want to file my taxes until this is corrected. What can I do? Please help!!