Ok ... there are 2 kinds of penalties ... late filing/payment and late estimated payments.
Late filing is when you file or pay the balance due after the due date of the return.
Late estimated payment penalty is because you didn't pay the estimated payments timely throughout the tax year ... you cannot just make one payment at the end of the year to avoid that penalty ... you had to pay the estimates as you earned the income. So your state is telling you that even if you paid the entire balance due with your return on the last day of the filing season you can still be hit with an underpayment penalty. You can even have a refund on the return and have this penalty applied.
Now if your income comes in unevenly thru the year and you paid the estimates according to that schedule then you can file an annualized penalty form ( in the feds it is a 2210-AI) ... check your state to see what form they have if any (and that would have been part of the state interview in the program as well).
