hello terroreek,
i worked with the guys from #debian-gnome on the issue and they have confirmed it.
<musca> Icons vanish if i toggle the setting "have filemanger handle the desktop"
<musca> if i immediate switch back then the icons will reappear.
<musca> if i wait more than 10 seconds then the icons don't reappear.
<pochu> ah, indeed
<musca> but logoff and logon let's them reappear.
...
<bigon> probably because nautilus exits?
<pochu> nope, it's still running
<pochu> and if you kill it, the background comes back
<pochu> oh wait I got the icons
<pochu> they are just on the secondary monitor
So now the talented people know about this weird issue and we can wait for a fix,
or downgrade libgtk-3-0
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=726562 .
greetings
musca