The afp2pdf advanced transform does not generate a blank back page (or mark the sheet as simplex in the page exceptions) if it skips from the front of a duplex copygroup sheet to a new sheet (so nothing is printed on the back). When printed on a PDF printer this causes the front of the next sheet to print on the back of the previous sheet. The transform does have the -completeduplex parameter, however that also forces the simplex copygroups to be duplex leading to extra page charges at the printer. An option which just makes sure duplex AFP copygroups always generate a blank back page if the back is empty or modifies the page exceptions to make the sheet simplex would be preferable.