I shoot a Phase Back on a V system, obviously I must use the sync cable, the observation that the CW winder does not show the fault points to some issue with the manual wind. I know it's the same gear but the CW has a rapid and firm action, are you winding perhaps deliberately and firm enough to fully complete the cycle?
If you watch the silver blade in action when you fire the shutter it emerges, that communicates with the back, it the returns flush to the back, on rewind it finishes the winding cycle slightly proud of the back. You should check the operation manually winding and with the CW, easily seen with a lens attached and the back off, to see if both methods match.
It is possible on manual wind to advance so that the shutter button will depress and the pin emerge without the lens shutter firing, it requires another 20 degrees of turn to complete the cycle. I think you should try another body if possible or send that one in for service the advance is a complicated system of gears and levers and may be out of adjustment but the CW forces it sufficiently to prevent the issue, at the moment.
The fault is definitely IMHO a timing one.