Stolen from the Big Foot web-site:
SI-Config will only work with COM ports that are numbered up to 16.
Each time that you plug a serial-to-USB converter device into a USB port that it hasn't been plugged into before, Windows allocates a new COM port to it. Even devices that appear to be straight USB devices may actually have a built in serial-to-USB converter and may be contributing to the problem. This includes all SportIdent download units, many 3G and 3G WiFi modems.
You need to clean up the unused COM port entries using Windows Device manager. A couple of tricks are required to make them visible in device manager: