F03B13 and R03B50 processing - does Program ID factor into reprocessing Receipts?

This is the scenario.

1. Receipts were uploaded into F03B13Z1
2. Receipts were processed with R03B551.
3. Receipts were successfully uploaded to Customer Record in F03B11.
4. Receipt records as viewed in databrowser for the F03B13 and F03B14 look ok and all the receipts in the batch seem identical.
5. We process the R03B50 using only 2 algorithms for all execution lists and versions of the R03B50 (all call R03B50D then R03B50F).
6. There are a group of receipts that did not apply since the invoices were not in the F03B11 yet.
7. The next day, invoices import and the R03B50 is run again. All Receipts are matching ok where appropriate except for a select few.