This sounds normal to me... and can also depend on how much you have your drive trimmed while on muffs, since the clutch dogs in the lower drive can be affected by angle and gravity. Do you operate on muffs with drive trimmed as level as possible (recommended, since this is less wear and tear on the u-joints)?
Does you shifter operate normally out of the water? (I rarely shift into fwd or rev while engine running on muffs, but you should be able to in order to see how the clutch dogs are working before putting the boat in the water). I usually do static shifter checks out of the water... again, with drive trimmed level (for the gravity reason) and the engine off (key REMOVED), I shift to Fwd, rotate prop CCW to see if it locks, Then do the same after shifting to Rev, rotate the prop CW and make sure it "locks". Then back to neutral, to check for free-wheeling. Only thing not checked out of water is the proper operation of the shift interupt switch, but this is not part of the topic this time.
Also, are you following the recommendations of mercruiser service bulletin 99-09 while operating on muffs?
Hope this helps. Happy boating!