Hi, don't think me silly, but have you set up multiple MIDI channels for layer A and layer B? I think it's called multimode in the global menu.
Another question: Are the two layers of your sound both mono and have unison with two voices turned on? If not, is your Prophet connected to a soundcard all the time? Perhaps the soundcard is sending back,m what it receives from the Prophet. You can check that, by going into the global menu and turning "local off" or by pulling out one MIDI cable.
HTH, if not, perhaps let us know which operating system versio you have. It should say that on startup.
Sorry, if this was far below your technical abilities, but better save than sorry.

Best wishes, Ffanci