Check both sides of the fuse under the hood. it allows charging one way and 12v the other. You can run a roadster without the 12v battery so I suspect either the fuse of the switch pack. I know some people are having trouble with headlights remaining on after a 3.0 which suggests the reprogramming either interferes with the switch pack programming or there is a component that interferes with its function. This is just a hypothesis because its not consistent. Either way the 12v should not be an issue even if its disconnected,