Windows – How to pass security issues in Vista

The Program Files folder and it's contents are read only for standard users. This is by design, and you'll find that this is the case on Windows XP as well. It's just that on windows xp, so many people run with administrator rights all the time that you might get away with it. If you ever want to distribute your app into a business environment, you'll soon find that it won't work on XP there, either.

The solution is to NOT place files in the program's executable folder if standard users will need write access. Put them in the Application Data folder instead. For most xp machines, that will be here:
C:\Documents And Settings\All Users\Application Data\Your App

However, that won't always be the case and it's a little different on Vista anyway, so make sure you get that path via the mechanism provided by your programming environment. In .Net, you can use the Environment.GetFolderPath() function.

As Oskar Duveborn said, it's very likely that what you're seeing is Vista's virtualization behaviour.

When a machine has User Account Control (UAC) enabled, standard users and non-elevated programs aren't allowed to write to the Programs folder. Windows instead silently redirects files to the appropriate subfolder of %AppData%\Local\VirtualStore (for example, C:\Users\MyUser\AppData\Local\VirtualStore).

If you browse the real folder in Explorer, you'll see the 'Compatibility Files' toolbar button, which you can use to browse the virtual store instead.

Note that this is only compatibility behaviour from Windows - your program should write to its own subfolder of %AppData%.

For more information, see this TechNet Magazine article.