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So, apparently Vista does something that is actually kind of smart. If a program tries to put preference files, etc into the "Program Files" directory, it dumps them elsewhere so that they are still going to be user specific. (This is all hypothesis!) Anyway I was trying to move my scores from WinXP to Vista for "Snoodoku" and this was the solution. http://www.wordofmousegames.com/forums/showthread.php?t=2134
Well, I found it myself, so figured I'd post the solution for future users.
Apparently, Vista merges two directories when a program is trying to store preference files in the Program Files directory. So the file was actually hidden away in C:\Users\RevRagnarok\AppData\Local\VirtualStore\Program Files\Snoodoku
More info from Microsoft.
