If this indeed happening, you need to contact CSD (Customer Support Department) for immediate investigation. Doing on this community site without seeing database is almost impossible.
Did you discover that neat 'feature' that PADS only verifies what is on the screen? If you aren't viewing the entire PCB when you click the 'start' button you aren't verifying the entire PCB.
Not sure it is a partial display problem, but i will keep it in mind for next design.
Highly likely it's the display. It's a very helpful feature. You can verify only the part of the circuit you want by either zooming to a window or turning off layers. No need to pick through hundreds off errors every time. But if you aren't aware of the feature, you can send out boards with errors.
I first make clearance verify, then connectivity, then plane, then clerance once again.
The second clearance verify doesn't give the same results as the first time.
No display problem, I think.
See on several board designs.