AppUp will always launch apps in the default AppUp store directory folder: C
rograms File\Intel\IntelAppStore\bin.
As a result it appears your app can't seem to find the needed files to run. Thus it won't launch from the store but it will run from the desktop.
Essentially, in your code you should do this
CString path = " C:\Program Files\App Folder ";
SetCurrentDirectory(path);
Here is a link on how to set the current directory.
http://msdn.microsoft.com/en-us/library/aa363806(v=vs.85).aspx
Also, can you ask them if you are calling the function LoadLibrary() or trying to set a path to a resource file/files location? If so, please ask them to set the full path of the file when they pass in the parameters.
Typically some developer use relative paths in the code such as \\AppFolder\\ResourceFolder\\sound.wav. Instead you should use the following: C:\\Program Files\\AppFolder\\ResourceFolder\\sound.wav