Do you have a question here?
I assume the government wants more money and if your CPA is baffled, (why use TT if you have a CPA?), then I'd guess the government is wrong in their assertion or you really did leave something off your income tax return and haven't told your CPA about it.
One item that comes to mind here that could cause this situation is a "same day" sale of employer stock - maybe a sale of stock for taxes due to the compensation created by you receiving the stock - that resulted in a 1099-B that you figure you didn't need to enter because the gain indicated there was "already reported on my W-2."
