Unless you filed really early in the season (i.e. anytime in January) there was unlikely to be a software error for that calculation.
As a wild guess...The one thing I can think of that could have been missed...or mis-entered by you into the software,.....that would be your tax-exempt bond interest. Those $$ do figure into the calculation.
Check that the total of all your box 8$$ (minus box 13) in all 1099-INT, plus all box 12 in all your 1099-DIV forms ...make sure that total adds up to what you see in line 2a of your form 1040. If line 2a on your 1040 is significantly lower than your manually-totaled amount, then it's most likely you didn't enter all of your tax exempt $$ when you originally filed.
(I've heard that there can be $$ from forms K-1 too with tax exempt $$, but I'm not familiar with that form)
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
