It seems that I only unpinned them from Start Screen, not uninstalled them properly. After some searching and uninstalling again, they're all gone now. The rest apps work fine whether I run them from folder Start Apps or from Start Screen.
I rarely check All Programs on Start Menu. I remember when I last opened folder Start Apps (not sure in what old version), all of the applications had the same icons, something like a sheet of white paper! I clicked on the folder today and found out all the applications have their own icons. Feel like I am behind the times now!
Btw, I seldom run Metro applications from the desktop, almost always go to Start Screen and run them there. It's much faster and easier to find them because they are arranged in groups.
Thank you both for replying.