I'm joining this thread because I have the same issue. Clean install of QB, fully patched, but the file I'm working with has 6000+ (!) invoices set to print. I can print all of them to a PDF, but QB crashes as soon as the print job is complete, and fails to flag the invoices as having been printed. 

Is there any way at all (maybe through the API? I'm willing to try anything) to bulk-mark the invoices as printed?