The sad thing is that the patents are not even on the filesystem, but on the workaround they had to put it to support long file names. And even that wasn't a novel concept - OS/2 had already added long file names to FAT, just in a different way.
Aren't patents exactly for protecting a particular way of doing things, instead of applying to concepts?
Not to defend software patents, I still think they're a stupid idea, but for patents prior art applies to the exact workings of something, not the general idea and concept.