I'll be interested to hear the explaination as well. Almost sounds like a snipe hunt, but I'm sure there's an explaination.
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Disconnect your RCA output leads and if you have XLR output leads disconnect them too. Place the leads of your multi meter on the RCA output connectors and measure for DC volts. Then do the same to the XLR output connectors if you have them. On the XLR connectors measure Pin 2 (+ signal) and Pin 1 (Signal Grd) then Pin 3 (- signal) and Pin1. Ideally it should be O volts or a few millivolts. Anything larger may damage to your speakers particularly if your amp is DC coupled.
Intermittent problems are among the hardest to run down. It could be an issue of a bad capacitor that only misbehaves when it charges to a certain point. Or it could be temperature related or tied to the type of signal. Cold solder joints are also suspect in this type of situation.
I'd measure for DC under all conditions - when it sounds OK and when it is misbehaving. There's a more than fair chance this is going to take some bench testing by a a good electronics tech.