Bug#646104: gnome-shell: transient windows are partly covered by the top bar and are not accessible

[Marno]

This is the case with all resolutions, I have a somewhat usable workaround.
Use this extension: 
https://extensions.gnome.org/extension/358/activities-configurator/
Set the panel transparency to 100 so you can see the top line of the 
menu and it will be clickable too.

It would be nice to have a real patch to this, it's not something 
isolated, it affects everybody.