I've tried every setting I could to isolate it. Effects off, LFO and Poly Mod settings at zero, filters set wide open, slop at zero. It only happens in unison. It happens with each oscillator individually, on any waveform, and in combination. It happens with any key mode setting, and any number of voices 2 or greater in unison. It doesn't happen in unison set to 1 voice. It's only noticeable with low frequencies, when either oscillator is tuned low, or with the sub oscillator. It's a slow cycle, that takes time to go from minimum to maximum volume for the low frequencies. The higher frequencies don't seem to be affected.
I first noticed it when playing a bass patch in unison, where the low frequencies seemed to disappear and then reappear. It happens whether I play short notes or hold one note for a long time.
It seems like the most likely explanation is a very slight variation in tuning or phase between the voices when more than one plays the same note. It sounds like the notes slowly going in and out of tune or phase, with the low frequencies canceling each other out, then combining to become loud, and back again. This is the first fully analog synth I've owned, so I don't know if it's standard behavior, or if it's unique to the Prophet-6, or unique to my individual unit.
It is a significant problem when trying to play a bass sound in unison. Having the low frequencies completely disappear is not good. I've tried auto-calibration already while I was trying to isolate the problem, but maybe doing it more will improve it.