My daughter uses my mini itx pc when she comes home from Uni but just recently it will partially lock up after about 10 minutes. The PC is still running, you can move the mouse and click on the start button but not actually click on the any icons or shut it down normally. I have checked windows updates and it seems to freeze 70%ish into doing the windows 10 fall creator update. I have tried manually installing the meltdown/spectre updates as well but it says they are suitable for that pc. Its been 3 weeks now and I'm no nearer getting it up and running properly.
I recently had something similar, everything looks like it should work, and two or three right clicks on the start button would open the options menu (that you can actually shut down or restart from). No taskbar buttons work, start menu doesn't work - but desktop shortcuts to flders etc. do ! Latest graphics drivers solved it, but then i went nuclear and reinstalled windows anyway (with latest graphics drivers first thing after windows).
I run into the same thing from time to time. Have you tried the usual ctrl+alt+del combo and then pressing escape to get out of that menu? It usually solves it for me.