ok... i did some 4 hour testing yesterday... the result is good and bad

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first: i had a rocksolid timing with temposyncing the analog rytm to MPC and playing tons of midi note and controller data of my prophet... i set the prophets clock to external and it also the sequencer was super stable and always in sync, even when i did heavy and fast tempo changes....
BUT: i wanted to record the prophet and layer the audio in audiotracks... as soon as did this, the machine crashed. i was able to repeat this failure 4 times... when i only use midi, internal programs and clips (including efx and q-links) everything is fine... as soon as i activate audiotracks (even just the monitor) everything gets crazy... midi sequencer reacted super delayed (almost 2 seconds latency when playing stuff into the sequencer), mostly internal erros when saving or shutting down.
as soon as i shutdown the unit (sometimes you have to do it twice, to get a "clear" shutdown) and restart.. everything is fine again.. maybe you also used audiotracks? so this could be a mpc issue... otherwise, it would come down to the old stupid questions, like: did you send midiclock and MMC-data to prophet? did you set prophets clock to MIDI/external and stuff like that

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