Eu tive o mesmo problema no Ubuntu 16.04 LTS (64 bits). Eu atualizei o arquivo ~/.vnc/xstartup
para parecer abaixo, trabalhei com sucesso para mim.
# 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 $HOME/.Xresources
xsetroot -solid grey
vncconfig -iconic &
x-terminal-emulator -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" &
x-window-manager &
gnome-panel &
gnome-settings-daemon &
metacity &
nautilus &
Referência: link