Believe it or not, I think that's actually normal in many cases and does not indicate a problem with the serial port.
Please try the following:
- Re-download the MK1 .upgrade file for beta13 using something like GetRight. This is to make sure it's not corrupted.
- Make sure it's the Mk1 version of the file, identifiable by "Car1" in its file name.
- Plug the Mk1 into the serial port.
- Unplug its AC adapter power.
- Double click on the Mk1 upgrade file.
- Only when the software prompts you to do so, and not before, apply power to the player.