Mike, you've mentioned speaker placement and room effect but haven't given any details as to either factor to help analyze what the problem might be. Paul Barton(along with Ian)was among those studying at Canada's NRC with Dr. Toole many years ago and certainly also designs fine speakers. The boominess you've described certainly isn't inherent to the M2s, although it's puzzling why there should be such a huge change from the M3s if the placement was nearly identical. Also, it can be assumed that you're not applying the loudness compensation switch on the PM660, which might inflate the bass response, although not to a "colossal" degree. Another hopefully safe assumption is that the jumpers on the M2s are tight so that the tweeters are actually in operation.
With just the present info it can be pointed out that to minimize the room boundary effects on bass inaccuracy the centers of the woofer cones should be at unequal distances from the two walls and the floor.
Enjoy the music, not the equipment.