So I did a Google search and found-out how to change it.
Just in case I forget - or somebody else finds this on their search:
Edit the RegKey
HKEY_USERS\.DEFAULT\Keyboard Layout\Preload
and change it to the appropriate value.The original post that gave me this info didn't contain all the keycodes.
So the keycode for Estonian layout is
00000438
, which I found here.