Dual monitors with one above the other?
Solution 1:
I will conclude that this is a Gnome bug (which I have filed), since this works in Unity. Also, I have tried using the open source nouveau drivers (which properly support xrandr), and the same thing happens.
Solution 2:
have a similar setup and therefore issue here but: if I get to get the external (upper) monitor as main one with the top panel than everything works fine. The downside is the process how to get the upper monitor to be the main one. For me, it takes a couple of active/deactive apply reapply... actions in nvidia-settings tool. Have not found any determinism on that one.
also to mention, at work I have Intel hardware and multimonitor-support works without issues.
thus it might be a gnome issue with how nvidia does its multimonitor-support?