Comment 8 for bug 108928

On the GNOME login, gnome-session has not yet set the keyboard (something it does badly when it is VNC, because it has problems listing available keyboards from the Xvnc session)
This is why the GNOME login works right when VNCserver use XDMCP ( vncserver -query localhost) (XDMCP has to be activated too)

So there is a temporary solution (that won't work if instead of XDMCP, you are uglily launching gnome-session...) :

When you are using XDMCP, VNC first displays the splash login.
At this time, through ssh, through the same account that has launched vncserver, save the keyboard map :
xmodmap -pke -display :1 > ~/xmodmap.map ( if your VNC display is :1 )

Then on the Desktop, just create a script that will load this map with for example nano.
---
#!/bin/bash

cat ~/xmodmap.map | xmodmap -
---

chmod u+x it..

This will allow you to get a correct keymap after you have clicked on it (you can even configure your session through the Session menu to launch it automatically)
This ugly hack is obviously just a temporary fix..