Be sure to vote for Game Pipe on Greenlight if you haven't already.
This release adds logic to better handle cases where multiple AppManifest files are present with the same Install Directory. This pattern appears to be used for expansion packs and editors, or other situations where game resources are shared between multiple applications. Now, Game Pipe will see these items as an inseparable bundle, and will move all the associated acf files along with the shared install directory.
The icon for Game Pipe has also been updated with a transparent background, hopefully this is less gaudy. You may have to restart your PC for the icon to update on your desktop.
Lastly, I've added logic to have the installer also download and install .net 4.5 if needed