The program files issue is not what you describe. In Vista, applications that save their settings in Program Files get redirected (invisibly to the application) to a subfolder of "C:\Users\[username]\AppData\Local\VirtualStore\Program Files\" named after the application.
See
http://www.microsoft.com/technet/techne ... FirstLook/ and scroll down to Data Redirection.
Therefore default installations do not work, becuase the ini files and the database are all inside Program Files. They appear to work in the application as long as you do not change user. Once you change user you get the original installed settings and database - it appears as if all your data has been reset.
Also problematic in this is attempts to backup and restore the database/settings files - what do you copy etc.
Recommendation is that settings files and data are not stored in Program Files during installation, but in All Users instead.