There is definitely a problem with the software. If you look at the 1040 worksheet the numbers will be correct there, however the IRA number is not being included in the gross total needed in 1040 line 4a, but it is included in the taxable total in line 4b. I'm using the Home & Business version which I downloaded. The Intuit corporate line is that the IRS instructions for line 4a are unclear & that what you see is a result of their programmers following the instructions.
Seems thin to me