Have you tried to disable and re-enable the Checkmate service on the machine itself? (In Checkmate 5.6 --> Administration --> System --> Keys and RF --> PC USB Downloader). Does the PC USB downloader still not get detected?
Are you running a Windows XP environment? If so, you may have to restart the entire system for the USB Downloader to get detected properly.
Try the above and if this does not fix the issue please contact Geosupport (via your reseller) and we can look into this further.