This is actually a problem for me too. I'm not running any MIDI data except for MIDI clock over a very capable MIDI interface with a very capable computer – if details are required I can provide them, but this really seems to be an issue with the Factor pedals. While Dan's suggestion of simply inputing the same tempo is likely to work for many users, this isn't a good solution for me. I want to be able to get MIDI clock from a drum machine which is being tap tempo'ed live. So you can see that there is no way for the tempo to be communicated to my Factor pedals without MIDI clock.
It also seems to me that the MIDI jitter is worse at higher tempos. Usually the Factors can lock on and not drift up to around the 90 BPM range – which is where they start to drift by a few beats at a relatively low frequency. Increasing the tempo makes the drift amount and frequency much higher…very choppy indeed.
This is actually a much bigger problem for those of us who sprung for a Mod Factor because the audible problems are so much more pronounced with those types of effects. I have yet to try syncing the Mod Factor to MIDI clock in order to see if it actually pays attention to the beats (so the tremolo actually goes in time and not simply at the same tempo) but I really hope it does. I did, however, have the opportunity to verify that the Mod Factor does drift when sync'ed to MIDI clock as the Time Factor does.
Speaking of sync and the Mod Factor (hope I'm not hijacking the thread here) the secondary LFO should really be in sync with the primary. Currently these run completely independently such that the effect is always fairly random due to the wave forms not starting at the same time. I can see this being useful too, but save for when the preset is not sync'ed to tempo. When it is sync'ed to tempo, both LFO's should synchronize to the tempo and start at the same time. You'll notice quite a few posters stating that they find the secondary LFO completely useless…perhaps this could change some peoples' minds.