Are you basing the timing of the LFO (in sync with sequencer) in PATCH mode on how it corresponds to the metronome? Did you do this in PERF mode, too? Or were you judging the tightness of sync of the LFO by its timing compared to the rest of the tracks in that sequence? If there are other tracks, how many?
It may take a little time, but if you post the main parameters - waveforms, envelopes, LFO settings, and filter settings - of the (User) patch in question, I'll try to re-create your situation on my XP and see if I can help. Or you could e-mail it to me. Of course, by posting it here, others could help as well.