Some questions:
Is this a plain Mamiya M645 with the insert, or a Pro or Super with the interchangeable back?
When you say the exposures were cut in half, do you mean the frames overlapped but a 6x4.5 area was exposed, or that you only got half of the 6x4.5 area exposed onto film and the other half was blank?
I think that taking the insert / back out and rewinding the counter might mess up the frame spacing (also, unless you have the interchangeable backs, didn't you lose some frames to being light struck when you did this?) However, I would expect that the full 6x4.5 area should have been exposed regardless of counter problems.
You can test whether the camera is exposing the full area by opening the back, setting the camera to Multi, winding, and firing the shutter on say the 1/2 or 1 sec exposure, so you can see what is going on and if the shutter is opening fully. (You need to set Multi so that it will fire the shutter even though there is no film to advance.)
There are a lot of different bodies and prisms, but on the M645, I think that you need to set the body shutter dial to the red dot for the prism shutter speed knob to take effect. Otherwise you get whatever the body is set at.
Excuse the question, but: were you using flash? The M645 has a focal plane shutter and max sync speed of 1/60, so if you use flash and set a speed higher than 1/60, only part of the frame will be exposed due to the way a focal plane shutter curtain works.