by Ken Task.
@Dan
Welcome. Got another idea ... something else to investigate. Have a 2.4.x+ with certificate and in a course active. Backup with no problem. Restore with no problem. The certificate settings are basic. In the problem courses with certificates, check to see if they have something in common in settings of the certificate ... like an image that was uploaded.
Otherwise, you are right, kinda annoying to have to remember to un-check the certificates every time one does a manual backup ... and of absolutely no use should you ever turn on automated backups.
'spirit of sharing', Ken