Sounds like this is related to the same defect I found related to rules porting. Some rules changes do not port properly, though there is no indication that they failed to port. A review of the Design Rules settings shows that the new rule is in place, but it isn't. Verify Design doesn't even catch the violations.
Thus, you are likely sending boards out the door that are violating rules, and you have no way of knowing that they have been violated. I hope your boards aren't crucial to public safety... Some of my boards have 1000's of nets and 8 layers. A visual review of every net on every board to catch the PADS errors is an impossibility.
I have had a SR in to Mentor since June 2014. The issue was acknowledged and turned into a DR. However, it is unclear why they have thus far failed to address it. Design rules are a function that is FUNDAMENTAL to the usefulness of these tools.