Oops, I edited my above post but it was actually after you replied.
Your major problem is an odd one but to answer your other questions (although none of this would likely cause something so drastic as cymbals 'disappearing...) here are some other tips.
Since you have a subwoofer, general consensus is that all other speakers (including the fronts) get set to small so that they don't have to work at trying to deliver the lower frequencies that your sub can do a better job of. Otherwise, you have a scenario called "double bass". You will find a few people who like this though for thier individual scenarios.
Also, check your crossover settings on your receiver. If you are already setting a crossover there, no need to set it again on the sub itself. It should only be set on one device or the other.
60 should be a very good crossover choice with M80s but it never hurts to experiment to see what works best in your individual room.
Some other things you might try for sound quality.
-- Calibrate your speakers so they are all equally loud via the auto-setup in the receiver or purchase a db meter and do it manually. You might be running the surrounds or the center too hot for instance.
-- Turn off any further auto-EQ calibration you might have done with the receiver. See how it sounds. If it sounds better, run it again. Choose which way sounds better.
-- turn off any EQ sound modes in your receiver. I'm not sure what they are called in a Pioneer.
-- Make sure all your speakers are wired "in-phase." That is to say positive on your amp needs to connect to positive on your speaker. In your case, you need to check the polarity between the Pioneer and the Nad as well.
-- Try a direct-stereo mode so that all you are listening to are the M80s. Process of elimination, if nothing else.
Quality can be a subjective thing but it puzzles me that cymbals are completely missing. Does it sound like you are missing all of the higher frequencies or was that just a single anomaly?
It could be a problem with the processor in your receiver or source device as well. Do you have access to other devices to start swapping out gear to isolate the problem?
With great power comes Awesome irresponsibility.