Ignore Penalty Check Box
There is a penalty date on the batch payments screen that is used when you commit the batch but it has nothing to do with the "Ignore penalty" check box. Penalty charges or late charges or anything else already on the bill will never be ignored. The date used to calculate the after due amount is the current date/time so if the current date/time is less than the bill run penalty date (if any) or the due date. In these cases the after due amount is the same as the due amount so ignoring it has no effect. The after due date amount is calculated (and can be ignored with the check box) is the amount accrued after the bill was printed and went past due without being paid up until it is paid. This amount can be waived until it is aged and added into the charges.