Jim,
Unfortunately this is a sticky windows operating system issue. Up until Vista it was fine if a program stored data in the "Program Files/BeerSmith" directory. Then with Vista, Microsoft decided this was a big security issue and pushed data to the "virtual store" without really telling the program it was doing it. Now, depending on what your user and security settings are you could have data in either location. Even better, the operating system can change the location where these files are stored without telling the program, so basically you change a UAC setting in windows and suddenly your data dissappears...
At this point I would probably just open the good files and copy/paste them over the old ones (i.e. replace your existing data using copy/paste).
I did fix this in BeerSmith 2 by storing all data in the Documents/BeerSmith2 directory.
Brad