What you describe sounds like the resonance of ported speakers or room interaction. I'm guessing.
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I'm not familiar with the ML speakers. If they have cone bass speakers, you might want to check to see if they are blown by turning off the amps and then gently pressing the bass speakers back with your fingers placed around the diaphram -- i.e., pressing on the cone, not the middle part. If you hear or feel parts rubbing together, you may have a blown bass speaker and you will want to contact the manufacturer or retailer for further instructions. Don't press them too far in, but they should move 1/4 inch or so. They will come back out naturally because of the magnetic charges.
If that's not it, you may want to listen to the parts of the room that might be resonating. Sometimes, the resonance does not come from the speaker itself but from something in the room that is being affected, like a heating duct, a vase or a loose board.
If that's not it, you may want to move the speakers around a bit to see if that may not lessen the bass interactions from where you sit.
The sounds you describe are not something that I found typical to live symphonic concerts. I have heard that from time to time from some (but not many) poorly recorded cd's.
"Sometimes, the resonance does not come from the speaker itself but from something in the room that is being affected, like a heating duct, a vase or a loose board."That's a very good point. This happens with our piano consistently when hitting certain keys. (It's a traditional piano, not electric.) Vibrations are activated at the noisemaker's resonant frequency, like during the Tacoma Narrows Bridge collapse we all saw in school.
"and (I) always using the same couple of pieces of music."
I'd try listening (to this music) thru headphones for the mysterious "thrumming".
A friend of mine played a first-generation master tape of organ music on my system. I heard, unfortunately, the sound of the church's forced-air heating on the tape and pointed this out to my friend (he hadn't heard it previously).
The point is that this limited sample of music may be flawed (i.e., contain the thrumming noise) and you are hearing it because your system now has the resolution to reveal it.
Thanks for all your responses. I have been studying up on acoustics and room modes, and have tried the test with the headphones. It seems as though what I am hearing is an inherent part of these recordings if not a part of the music itself. I have also contacted Krell and Martin Logan and their responses have echoed what I've heard here. I've have some suggestions from them for a few inexpensive things to try to decouple the speakers from the space and to test whether there may be any issues with the equipment.