I’m at home now so I can’t try them per se, but I do know that connecting through VNC and using terminals does not cause problems. And I still use Gnome and Gnome Terminal over VNC, but it doesn’t seem to be Gnome 3 (or at least not gnome-shell). I say that because the top bar is replaced with a traditional menu, putting the mouse in the upper-left corner doesn’t do anything, etc…
My xstartup is:
#!/bin/sh
# Uncomment the following two lines for normal desktop:
#unset SESSION_MANAGER
#exec /etc/X11/xinit/xinitrc
-x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup
-r $HOME/.Xresources ] && xrdb $HOME/.Xresources
xsetroot -solid grey
vncconfig -iconic &
xterm -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" &
gnome-session &
So perhaps it is a gnome-shell issue? Are there composting things turned on that I can disable (I hate all the desktop effects anyway and turn them off whenever I find a way to)?