I’m having this same problem. But can’t blame the MIDI clock because it is receiving clock — from a TimeFactor! The PF does receive tempo changes correctly and has consistently since I set it up. But Harpeggiator only seems to work correctly with Tempo Off. I do need it to sync to the clock because everything else in my setup, including looper, is synced.
(To be perfectly accurate, the clock signal is originating in a ModFactor, then passed thru the TimeFactor to the PitchFactor; and then out to a Nemesis Delay and then looper.)