Reproducable on both RHEL 7 (4.5.0post-5097) and Fedora 23 (unknown version).
Client: 4.5.0post-5094 for Wyse Suse Linux SP3.
I was using two screens of different size, the smaller one to the left of the large one. From an xterm profile, xrandr reports the same monitor settings as the client does locally.
Once logged in to a Gnome profile, the screens have "switched places" and marked the right screen as primary. xrandr says:
VNC-1: 1600x1200+0+0 primary
This means that gnome believes that the left screen has a 1600x1200, so it overflows the smaller screen and spills out onto the larger screen, which is only partially occupied by the smaller resolution.
This happens with an empty home directory, so it's unlikely to be caused by residual settings from using gnome in another setup earlier.
Perhaps the information here is useful?: