FLAC support was not natively included with the Fuze when it came out. It was added in a firmware update. Seems to me I remember there might have been problems when the FLAC support was introduced, but I don’t remember the details.
Does your Fuze have the latest firmware update? If not, it would be worth updating it to see if it corrects the problem you’re having.
Edit: Another thought . . . Some older versions of WMP don’t handle FLAC. Rather than trying to ‘sync’ these files with it, why not just drag & drop them onto the card (and/or player) manually?