So it sounds like the original problem was the engine running too fast after start-up: that will prevent you from engaging drive. I suspect things like the side stand, slopes, etc, are red herrings.
The bike has a cold start fast idle, so I guess you could get this problem if the bike actuates the fast idle when the engine is warm. Alternatively the throttle is being held open by a sticky or maladjusted cable.
Very interesting mystery! I wish I could make a useful contribution......