Apparently Quickbooks is unable to listen to it's users.  I have this problem. Sometimes these instructions work, sometimes they don't.  The bug/problem lies after the invoices, bill payment stubs, whatever are printed. Sometimes QUICKBOOKS does not display the confirmation box that the forms have printed correctly.  If this happens, QUICKBOOKS does not mark the forms as printed even though they were.  My experience is that if you choose more than ~500 forms to print to PDF that this will occur.  Once the confirmation box does not appear, you must close QUICKBOOKS and restart or you will never clear this bug.

At this point I can get rid of my invoices but not my bill payment stubs using this method.  The repair software that INTUIT is pushing does not resolve this problem in any way, do not waste your time.