I can't help you really on this one, other to confirm that I used exactly the same approach with an external USB floppy drive (on XP) for my Fat Frog and had no issues. I'd have to say it was rare for me to re-format a floppy - I have a load of disks I use that probably came pre-formatted for PCs, although I know some I have wiped by reformatting using both the desk and the USB-floppy drive and I don't recall any issues. Maybe I'm one of the lucky ones since I've never had any issues with the floppy drive in my FF, while others report they do. Since you have a Mambo Frog, which was one of the last in the series to be released, I'd expect your drive to be one of the later ones - early Frog users seemed to report more issues.
Regards the Fixture Files - it goes without saying that this database is now much bigger than can be fitted on a floppy, so I make the assumption you have a customised cut-down version of the database!
If you get nowhere with the floppy, then you might want to look at swapping out for a paged USB solution. This was discussed recently here: