I did some more digging, and it turns out that this only occurs if a desktop file does not have a Type specified for the Desktop Entry. Adding Type=Application for compiz.desktop solved the problem for /usr/share/applications.
I did some more digging, and it turns out that this only occurs if a desktop file does not have a Type specified for the Desktop Entry. Adding Type=Application for compiz.desktop solved the problem for /usr/share/ applications.