I recently reinstalled Vista and just discovered something. I was looking for some fla files on an FTP site via CuteFTP and couldn't see them, then looked for a local copy on my drive using Windows Explorer and once again couldn't see them. I then searched my drive for *.fla using Windows Explorer and could see them all right where I had just looked. I later saved a new fla file and have no trouble seeing it at all.
I have "Hide extensions for known file types" deselected and "Show hidden files and folders" selected in my Folder Options. I am running Vista and CS4.