Well specifically the FAT32 patents. They are going against a company not just for it's own technology, but for using a technology that is freely available in Linux.
I reckon the FAT32 one was thrown in for the sake of it, you'll notice there were other patents they were filing against. Microsoft hasn't previously sued over FAT or FAT32 (IIRC) but the commentators on slashdot think that's because it's likely the
FAT patents wouldn't stand scrutiny.