So this isn't really a problem for me, but I am curious as to why this is happening. My guess is that it has something to do with permissions but I am not sure. It works exactly as I described. Whenever I log in and click on a desktop shortcut or folder it doesn't open but when I open nautilus myself and just close it then all the desktop shortcuts begin to work as expected for the rest of the session until I log out and in again.
Would appreciate any help as to why this is happening and how to fix it?