Processing A/P Prepayments to Invoices not Working when writing a check

I have processed a prepayment a month ago and am trying to match it against a current invoice I received this month.  I have gone into speed release and approved the invoice and the prepayment for the same vendor.  The prepayment is less than the invoice amount.  When I run create payment group it is only picking up the invoice and not the prepayment.  If I process the payment as a wire instead of a check it picks up both the invoice and prepayment and nets the amount.  Has anyone encountered this problem and have a possible solution for me?