Just gone and read Wiki (search FAT licensing) at http://en.wikipedia.org/wiki/File_Allocation_Table
And it seems you should not have a common namespace for short and long filenames - i.e. a readonly implementation where a file can be open by its two names (when it has a long filename) would be covered by the patent.
That is what Linux VFAT do - moreover Linux VFAT is R/W.