No, haven't noticed anything weird at my home setup (syncing a rytm + OT, merging seq data with OT's MIDI out). OTOH we had an offset syncing to an LXR drum machine yesterday.. I needed to nudge seq data to get the downbeats locked, but once compensated, the sync was OK.
I'll do some more rigorous sync tests tonight. But at this point I'd advise not using audio tracks, they seem to cause issues with many things on the MPC, wouldn't be surprised if the issues even affected sync?
For you, maybe OT + toraiz is the way to go..? If you want good sounding samples and OT midi sequencing features are enough for you, that is. For me, the MPC sequencing workflow is too sweet to ignore, been a long time since writing/programming felt so effortless! It almost feels like the machine makes the beats by itself
PS: If you dig the vintage mode fx, try stacking them.. inserting four consecutive instances of, say, MPC60 emu, sounds even more crusty IMO