No need for me to repeat the "PF straight out to MIDI monitor" test (see reply above). 

I hooked a MIDI cable directly from the PF's OUT/THRU to the MIDI IN of an ancient drum machine [Yamaha RX-7].  A few spins of the encoder, and a START message kicks in the drum pattern.  I went in to the PF system settings, left the OUTPUT on THRU, and set both the CLK IN and CLK OUT to OFF.  I still got a START message to kick in the the drum machine.  I went through a few dozen variations on that theme.

You have to have a MIDI cable inserted in the PitchFactor's MIDI In jack to reproduce this, and I believe that a MIDI clock signal also has to be present on it (whatever the PF system clock settings are set to).  The corrupted clock theory is gaining credibility, but it's not just a Windows problem.

I think that's enough wear-and-tear on the encoder knob for one evening.