Create Additional Pay Separate Check

I am doing some testing with Additional pay and noticed that if I setup a new row in additional pay that includes a Sep Check Nbr for a payroll that is already started (Pay sheets created, first calc run), the pay calc does not create the separate check and pull the additional pay into other earnings. Also, there is no error or warning. If I go to the pay line and manually add a new, as a separate check with the same Separate Check number, before running the calc it will bring in the earnings. Side note if you have already run the calc