I had no trouble doing this, but then again mine is Mac formatted. See my battery replacement.
http://www.ifixit.com/Story/9597/New_Battery_for_Flash_Converted_G4_U2_iPod!
I formatted the card when I put it together and when I plugged it in I restored it.
Are you noting which pin is pin 1? Considering that there are more pins on the adapter plug than on the cable? Does your version have pin 1 marked? The extra pins should fall on the left side.