Windows 7 Shortcut IssueFollow

I recently had to do a fresh install of Windows 7 because my Vista copy was acting up. Anyway, I'm running into a strange error now... Whenever I go to install a program it assigns the wrong folder in the target making the shortcut invalid.

Example:

Installation folder is C:\Program Files
Shortcut after creation points to C:\Program Files (x86)

It's only a minor inconvenience, as I just have to change the target. Otherwise the programs run perfectly fine, no errors. It's just a little bothersome as I always have to change the shortcuts to make them point directly. The "Start in" box displays the correct path, it's just the "Target" that always displays the wrong location unless I change it manually. Any idea why it's doing this?

If it helps I found an error in a registry key that at one point read "%ProgramFiles(x86)%"
when it should have been "%ProgramFiles%". I've since changed it to the correct value but this still happens. It was caused when I was trying to change the default installation directories for installed programs via the registry. It didn't work out so well so I switched it back to the default. Little did I know I accidentally left the CommonFilesDir pointing to "C:\Program Files (x86)\Common Files". After realizing my mistake I changed it to the correct path (C:\Program Files\Common File) and rebooted. The problem however still persists and I'm not really sure how to fix it.

This was under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion by the way.