How are you sure that the engine is firing on both modules? And do you have a conventional rotary switch with spring loaded start position or are you running toggle switches for each module p-lead?
I can't think of anything that would cause the engine to run on both modules or not at all in the manner you're describing. I'm assuming your wiring is conventional.
I've just been through my Rotax ignition system thoroughly (not on RV) and the symptoms you're describing are puzzling, as you say.