The estimated period you put a payment in determines where that payment flows to calculate whether or not an underpayment exists.  If you pay it after the due date, and the program allowed it, the payment would flow to the wrong place and the calculations wouldn't be correct.  If you made a second quarter estimated tax payment after the due date, it wasn't really a second quarter estimated payment - it was a third quarter payment.  Just  adjust your estimated payments so that the dates match the payment period.