Try this just to see what happens. Boot the laptop. Using the RUN command from the "start" button, enter the command MSCONFIG and hit enter. When the MSCONFIG menu appears, select the "start-up" tab. Un-click everything. (disable all). Select "apply",,, then "OK",, then reboot.
At Boot up, you will see a prompt saying the "config has changed" . Click the box that says "don't show me this again" and hit OK..
Now plug in the dongle into the USB port.but don't plug the dongle into the bike. Turn the Run/Kill switch on the bars to RUN and the ignition key to OFF. Plug dongle cable into bike. Launch Super tuner software. Turn ignition key to ON.. Do you see the Super Tuner connect ion go from RED to Green.