Here are the MIDI Clock settings from page 14 of the manual:
4. MIDI Clock Mode: Sets the synthesizer’s ability to send and receive
MIDI clock messages:
• Off: MIDI Clock is neither sent nor received
• Master: MIDI Clock is sent, but not received.
• Slave: MIDI Clock is received, but not sent.
• Slave Thru: MIDI Clock is received and passed to MIDI Out
• Slave No S/S (no start and stop): Receives MIDI Clock but does not
respond to MIDI Start or Stop command.
Most DAWs send a MIDI Start command to connected MIDI devices when playback is initiated. The Prophet Rev2's Poly Sequencer responds to MIDI Start commands when synced to external clock, except in the "Slave No S/S" setting listed above. So, you either need to configure your DAW not to send MIDI Start/Stop commands to your Prophet Rev2, or set your Prophet Rev2 to "Slave No S/S" for the MIDI Clock global.