Cannot upload new scripts to HDC2460

Does anyone know how to fix being unable to upload new scripts to the controller?

From the perspective of RoboRun, everything looks find when I build the script and upload it, but when we run it a previous script that was uploaded to the controller is being run, and then my computer loses connection with the controller while the script is running. We need to pull the power and reconnect (but no luck uploading a new script).