Your link appears old. Newer info from the same source, couldn't these be some of the patents he's referring to?
http://news.com.com/Microsofts+file+system+patent+upheld/2100-1012_3-6025447.html
Microsoft's file system patent upheld
Two patents covering one of Microsoft's main Windows file-storage systems are valid after all, federal patent examiners have decided.
Thanks for the update. I should have found a better example.
FAT has been around since the 80's. Isn't patenting it now just a little too late?