I had something similar and got over it by:

1). Deleting the device from the Devices and Services node then close MMW
2). Quick format of the device then re-open MMW
3). Sync just one Playlist or Album to check files are where you want with right prefix

I use \Music\<Album Artist>\<Album>\<Disc #><Track #:2>-<Title> to get 101-The Wall Street Shuffle.mp3 in the G:\Music\10cc\Sheet Music\ folder. Also, I check that the album art is in place

4). Now crack on with full sync

Hope this helps

I created a USB drive for my wife's music, when i tried using it I decided that the File Locations setup was awkward, so I went back and changed it in the device configuration. I deleted all the files from the USB drive, but when I do a sync it keeps using the old format, not the new one. I exited and restarted MM5 to no avail. I remove and reinserted the drive, as well a put it in a different usb socket all to no avail. Any idea how to get it to use the new settings?