I have the same issue. I am using QB accountant 2018 with Wellspring Software's Print Boss for check writing. I wonder if any of these details are causing the problem. It would seem unlikely, as Print Boss is a printer driver...

Perhaps the reason is that I click OK on the QB dialog box that says that the check does not need to be reprinted BEFORE I  allow Print Boss to print the check. Would that mess things up, because QB has not "received confirmation" that the check has been printed from the printer driver? Does this make sense to anyone?

I am out of my field here, trying to explain computers when I am an accountant...