It has everything to do with the light since the bike only knows what gear it's in after the GiPro tells it. The GPS sends it's signal not to the ECM any longer, but to the GiPro. The GiPro now tells the ECM what gear it's in so that the programmed tune for only 4th and 5th gears are used. It also tells the ECM when it's in neutral so that the neutral fuel map is used and the light is turned on.
I hear you. My Gipro displays wrong gears in different gears and displays gears in neutral but I always have a green neutral light when in neutral. Power reset and using the "learning" procedures doesn't correct a thing. I've removed and cleaned the GPS and still get the same results. I've checked all connections too.
Based on your theory my GiPro is sending the correct signal to light my green neutral light when in neutral but at the same time it's sending a faulty signal to my Gipro display to display some crazy gear when I'm in neutral.
It worked great for about 6 monthes. It's a cool gadget when it works.