Are you sure you don't have MCACC autosetup adjusted for the m40's, and have not rerun it for the m60's? You may want to reset the receiver and start over. Also, if your using the EQ part of the setup, turn it off, it will make the speakers sound worse in my opinion. The auto setup is good for dB levels, distance, and polarity check, and that is about it.
Do you have another receiver, or can you borrow one, that you can temporarily try to rule out the receiver? You have a strange issue going on, hope we can figure it out, if not Axiom I'm sure will help you.
If your careful, there is nothing wrong with removing the drivers to make sure everything is correct and that no wires have jiggled loose. But if your having the problem with BOTH speakers this is unlikely.
You also don't mention how you have your receiver calibrated and crossover settings set for the lows?
