Not 100% sure if this is the same issue as what you're having but I traced my issue with the focuser not wanting to stop back to the FCUSB needing to be on a powered USB hub. If I try to run straight from one of my computer's USB ports to the FCUSB I would get this run-a-way in which the FCUSB LED light would remain green and the focuser would continue to move either in or out don't know which. The only thing I found that fixed it was using a powered USB hub. Not sure if your issue is the same but that seemed to have fixed my issue I had. It's as if the FCUSB needed more voltage/power than what the standard USB was able to supply.
Mark