hmmm, i'm not sure how the card reader interfaces the CF card to the PC.
just to be sure, (i did pretty much exactly what you're planning to do) i had the CF card in an IDE adapter, attached to an IDE to USB adapter to connect to the PC, so it definately shows up as a hard disk type device...
you'll probably be fine, but thats just what i did and it worked out ok for my A600 :-)