I have found the full texts for the patents for FAT. The links are very long, so I expect them to get clipped. Regardless, here it goes anyway.
http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=...
http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=...
http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=...
Those are all three patents listed by the MS FAT patent notification page at MS. I note how their claims arent specific about what kind of 'memory storage' the FAT structure is located in--- MS is being really paranoid about it.
Still, IANAL, but I would say this is grounds for an equitable estoppel. MS has allowed royalty free use of FAT for how many years now? How many industries rely on FAT support, as a De-Facto standard for floppies and flash media? Sounds like a textbook case for Equitable Estoppel.
http://www.nolo.com/definition.cfm/Term/7F1E56D5-7EC1-4CEB-86B3943F6990FF77/...
(First item)
I would bring this to the FSF's attention.
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Wierd_w