After reading this thread, I have two questions:

1) What report are you using to generate the positive pay file for your bank?

and

2) Is there a report that can be generated to show "Vendor Name" and "Print Name on Check"? If so, then one could possibly clean up all  Vendors where "Vendor Name" and "Print Name on Check" do not match. It might require some effort, but it would address the issue of not being able to create a positive pay file with the print name on check field.