I hope you are able to find the issue. I would think that this sound could be hard to hear in a rock band rehearsal unless you are specifically listening for it. I assume you are close-micing the amplifier because the drums and so forth are so far down in level on the sample you posted.

Something unintentional is certainly going on. The intermittent nature and appearance in the track where its not actually the hot section of the signal is going to make it hard to track down. Time to see if you can isolate it without the pressure of a rehearsal going on, in my opinion.

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