To grunt: Did your receiver set all your speaekers to 40Hz or just your M3s.
The only speakers either of my receivers ever set to 40Hz are my M80s.
Below are the ranges that my Denon 2807 and Onkyo 3007 have set my speaker
in and I've run Audyssey dozens of times in three different rooms:
M80s 40-50Hz
VP150 70-90Hz
QS8s 60-100Hz
M22s 70-80Hz
I'm suspicious that something is wrong with your equipment setting all your
speakers to 40Hz. You might want to post in the Audyssey thread over at AVS
and see if they have any suggestions.
Just setting everything to 40Hz is not in itself a problem because you can
always raise the crossover setting w/o negatively impacting Audysseys
performance. However, if the system is not correctly identifying the -3dB
point of your speakers then there may be other things it's not doing
correctly.
