That's strange, Windows has decided that all your apps are installed as public which means if you set up another account they'll see them (in theory) whereas if they'd been set up as private then only you would see them. Yours seems to be the wrong way around.
I'm not sure if it's the Microsoft account versus Local account that's screwed things up, you could try creating another (local) account and see if that account can see them in the desktop folder.
Alternatively you could select everything on the desktop and hold down ctrl while dragging to your folder to create copies as suggested earlier by yorknomore. I would then try installing something else (absolutely anything will do) and see if it creates a shortcut on both.