The electrons are revolting against being forced to work with the tubes.
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I would ask Rogue. Since it's not there when you put on the mute switch it's not in the amps. While it could be tubes, it also could be a capacitor or even a resistor which only exhibits this behavior when it gets to a certain temperature. I had a similar problem with my JP80 preamp a few years ago, it took forever to find the problem (was a resistor) because to get to the problem component we had to take off the bottom plate, and when we did that it cooled off the resistor and stopped the problem. A good technician should be able to find it, but Rogue is best equipped to do the trouble-shooting.
Depending on your listening habits, you could be well over 3000 hours on the pre-amp tubes since 2001. 10 hours per week for 6 years = 3120 hours of on time. 20 hours per week for 6 years is 6240 hours and 30 hours of on/listening time per week is 9360 hours over the course of 6 years.
Since the problem goes away when you place the pre-amp on mute, you know the issue is not in the amp. I think replacing the pre-amp tubes is the next logical step.