Looks like I have stumbled across a bug in GP 2016.
Our AP team entered several payments using the same payment/check number (duplicate checks allowed). When we went to apply them, we select the correct one, but GP will pull the first with the matching check number. So we have three payments, we are trying to apply the third, but when we select the payment it looks like GP is pulling the Payment into the Apply Payables window by CHECK NUMBER, instead of the actual unique value VOUCHER NUMBER.
If we use the arrows to "page" forward and back, the Unapplied value in the window changes depending on which of the duplicated check numbers it happens to pick.
We are going to void the duplicate payments and re-enter with unique numbers, but the PM Apply Payables Document window should pull in payments by voucher number which is the actual unique identifier.