When you say "Card Reader", are you saying you have a USB SD memory card reader?
If so, does it work in Windows? (go to Windoes Exporer, click on the E: or whatever drive letter it comes up as, and see if you can copy any file to it or from it). If you can't, then the problem is not related to Garmin or Homeport, it's your Windows/memopry card reader.
If you can see and use it in windows, then call Garmin tech support, I'm sure they can assist you.
"MACHRIA" 30 Rampage Express, 315 Yanmars