I finally got some time to experiment with this. If I make a new Logic document, add the Prophet V2 (2.5.3) and play a part while using the sustain pedal, everything seems to be fine. As soon as I close the document and re-open it, the sustain pedal messages are read backwards - that is, where there was previously sustain, there is now no sustain and vice versa. The solution is to go into the midi information and reverse the pedal 0 and pedal 127 messages. This makes the part play correctly, at least until the next time the project is closed and re-opened. At that point, the same problem crops up again. This creates a bizarre effect where a sustain pedal On message is 127 the first time the Prophet V2 is instantiated, but is 0 when the project is re-opened the first time, then back to 127 when the project is re-opened the second time and so on.
When I use the same project and replace the Prophet V2 with the Jupiter8V2 or CS80V2, everything works as expected every time I re-open the project.
The biggest bummer about this bug is that I won't use Prophet V2 on any more projects until this is fixed. It's too much of a PITA to change all the sustain messages in a project every time I open it.