Connecting the Prophet 12 via USB
When you first connect via USB, the Prophet 12 may occasionally ignore the system exclusive MIDI "Patch Dump" requests that Patch Morpher sends. A special work-around has been implemented in the application: when you first connect, play some notes on the keyboard so that app knows which MIDI channel to use. If the app requests it, please power-cycle your Prophet 12 (which takes seconds to reboot!). Everything should work flawlessly after thereafter.
Alternatively use a suitable MIDI interface as there are no problems with the MIDI implementation itself.