Apparently, on some copies of Vista the operating system intervenes and even though the TD thinks it is saving files to the same place the software is installed ("C:\Program Files\The Tournament Director 2" by default), it actually saves somewhere else. Try looking in:
C:\Users\<your login name>\AppData\Local\VirtualStore\Program Files\TournamentDirector
Might not be exactly that, but that gives you somewhere to start.
Not sure why it does this, or on which versions of Vista (there are so many versions...). It doesn't do it on my copy, so I don't have any first-hand experience with this.