I use Gnome 3 on my client, and run XFCE on the server. I have the same problem: even when run fullscreen (launched fullscreen), an area at the top of the screen corresponding to the *client's* Gnome 3 bar does not respond to clicks. I have my server's XFCE menu on the left, so this means window decorations and title bars, as well as a bit of the top of the menu, are unresponsive.
Toggling full screen with ctrl-alt-f (off and on again) doesn't help. I also see the black/white cursor problem described.
Client: Ubuntu 16.04.1 LTS, x2goclient 22.214.171.124-0~1205~ubuntu16.04.1 (from PPA), Gnome 3.18
Server: Ubuntu 14.04.5 LTS, x2goserver 126.96.36.199-0~1064~ubuntu14.04.1 (from PPA), XFCE 4.10.1-3ubuntu5