Maybe not a direct answer to your question, but...I just ran into a similar issue - I completed my taxes at the beginning of February but did not file them - small Missouri refund and small amount owed to IRS. About 2 weeks later, I logged back into TurboTax and my Missouri refund had increased dramatically. After a lot of research, I redid my Missouri taxes on the downloadable-fillable Missouri tax form 1040 just so I could see how TurboTax was coming up with its numbers. Everything matched what TurboTax was showing me. So I get a big refund! Awesome.
My biggest pet peeve with tax software is I can never see the calculations behind the final numbers - especially this time, for the Public Pension deduction figure - I had no idea how Turbo Tax got to this number. A great addition to TurboTax would be to somehow show the calculation processes.
