Every time I run my system (Ubuntu 16.04/16.10/17.04 with GNOME installed) icons on the desktop are under top bar and when I open any window they come back to their position before turning system off. I reinstalled system many times and on many computers and it didn't help. I recorded and uploaded it on YouTube - link below.
I had the same problem after reinstalling my OS (Debian 9, Gnome 3.22.2). What solved it, was to play around with Gnome Tweak (Tool). As I did not do this with "scientific rigor", I can only guess it was switching off and on the option to have icons displayed on the desktop or activating hibernation when the lid of my laptop is closed, which automatically set a program to load on start up and thus might only make it look like the problem is solved.