What do you mean you sent a check for it? Did you send a separate check for it? The penalty was already included in your tax due or had reduced a refund. And it is just an estimate so it is possible for the IRS to recalculate it and send you a refund or a bill for more.
If you had a Tax Due. The Tax Due on 1040 line 37 is line 24 Tax minus 33 Payments PLUS line 38 Penalty.
If you had a Refund. Take the overpayment on line 34, subtract the penalty from the amount you would otherwise enter on line 35a or line 36. Lines 35a, 36, and 38 must equal line 34.
