On my Mopho Keyboard, you can hear a subtle phasing effect on the initialisation patch if you listen closely. This patch is very similar to the one on the Rev 2, just two saw oscs with the filter wide open. I found that Osc 1 was Fine Tuned to -1, and Osc 2 was Fine Tuned to +1. Even when setting them both to zero, the phasing is still present, though to a lesser extent. I'm guessing this is just because of slight variances in the two oscillators.
Could it be that this phasing is what you're hearing?
It seems unlikely on an Init Patch, but maybe could there be something assigned to modulate the LFO 1 Amount such as the mod wheel or aftertouch? You could also try changing the mod destination of the LFO to something else, such as Cutoff, in order to see if it is definitely modulating at a zero amount.