Did you already get a new harness? That seems to me what it is. Something in the ignition sequence shortens out but not Soon enough for the bike not to turn over. Then you turn it off and the computer recognizes it. That's my thought process at least.
Hey dont feel bad I did the same.e thing. I let the smoke out. Mine turned out to be the ground wire going to the fuel tank. I ran new wire from tank to negative terminal on battery and worked fine after that
Also where is this main fuse located