"Root" is the highest directory on any device. In the case of the card, it's where you arrive when you first double-click on the card in explorer. You should make a directory called something like "Music" and put your actual media files into it, not the root.
Format your card, then put just the .fw file above on the card. Do the update, then reset. Then, format your card again, create a directory called "Music" and drag your files to it. Finally, insert the card and do the library update.
This is pretty much standard procedure on any flash media device. Actually, there are limits to what a root directory can handle on a lot of file systems, so you should never drop a ton of files into the root.
The structure I use is:
ROOT -> Music -> Lossless -> Artist -> Year. Album -> Track#. Title - Artist.extension
ROOT -> Music -> HDA -> Artist -> Year. Album -> Track#. Title - Artist.extension
ROOT -> Music -> DSD -> Artist -> Year. Album -> Track#. Title - Artist.extension
ROOT -> Music -> HDAFromDSD -> Artist -> Year. Album -> Track#. Title - Artist.extension
ROOT -> Music -> Lossy -> Artist -> Year. Album -> Track#. Title - Artist.extension
ROOT -> Playlists -> Playlistname.m3u8
Even on imaging cards, the images are saved in a directory called "DCIM" since early FAT/FAT32 cards had a limit to the root.
