Hi Ryan,
What does your Synscan Hand controller show as the version now?
What is the Hand Controller V model v3/v4/v5?
It maybe the wrong version software for the handcontroller?
Once validated its the right software version - can you go through the upgrade process again?
Firmware: SynScan V5 Hand Controller For All GOTO Mounts, Version 6.00.06
Please note that this hand controller firmware is applicable for those hand controllers with version 6.00.00 or later only. This firmware is not compatible with SynScan V4/V5 hand controllers with version 4.xx.xx. If the hand controller is with version 4.xx.xx, please do NOT update with this firmware. The outlook of the hand controller with version 6.00.00 or later is identical to the SynScan V5 controller with version 4.xx.xx except that the LCD modules are different. Both the firmware with version 4 and version 6 have the same functions and features, we will keep updating and maintaining them simultaneously.
http://skywatcher.com/download/software/
When I upgraded I had alot more issues finding a serial to usb converter to work with the Hand Controller and Laptop - this was for v4 going to 4.39.
Hope it helps,
Mel