Yes the engine and trans are controlled by computer. Even more interesting: The throttle is controlled by the computer as well (throttle "by wire").
When reading your story I was suspecting either the foot pedal position sensor or the throttle position sensor but since you were able to clear things up by rebooting the system (so to speak) perhaps you found an odd corner case in the ECU code. (Although I find that somewhat surprising given that the engine controllers are usually rock solid--especially when you consider the lead time of the software and how long it took to get that technology in to RVs.)
Glad to hear you got it sorted out...
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