Indeed.
The right course of action would be to:
1: determine with certainty that there actually is a problem. Take some of those tedious test shots of a ruler that runs away from the camera to see how much back/front focus you have with several lenses.
2: verify correct ground glass calibration using a piece of ground glass (or similar/equivalent) at the film gate, with the camera on a tripod and the back open so you can compare what the film 'sees' vs. what the ground glass shows.
The Mamiya 645 cameras are somewhat notorious for having the mirror go out of alignment. You notice this in the tests above as focus being spot on either in the top, middle or bottom of the frame, but not in the other two areas. This can also explain why you think you're seeing this with one lens only because you may have a habit of focusing on a particular part of the frame (bottom, middle or top) depending on what lens you use and what subject matter you have in front of you.
In any case, the first step is to verify what's really going on, objectively.