Okay, this might be the solution here, took me a while to pull this outta my memory bank...
Question: When did you get these mackies? 6Years (Italian)
If you read on over at the mackie boards you can see some other users occasionally have these problems, the issue, the temperature sensor goes haywire and causes the unit to shut down at times. It may stop, it may continue, it may continually get worse.
This problem has been reported on some models (and batches/runs) of mackie's products. However I'd call mackie (warning: long wait time may occur) to find out exactly if this is the problem.
Looks like I'm gona have to
Question: Did it seem as if the speakers were ducking (ie lowering volume intentionally) as if it was lowering during certain notes, frequencies?
Yes, It did seem slike the Volume was dropping, This was during Dinner, no major bass notes (frequencies)
Try this, have that speaker on and turn the gain all the way up, and try what you did to get it to clip or limit. Be sure to play the music at performance level when you do. Also experiment with the low-cut feature, on and off. This could revel some explanations.