Please check if your graphics card is OK, type this:
glxinfo | grep render
and you should get answer which contains text "direct rendering: Yes"
Maybe you will need to install package "mesa-utils" for this.
Then please start `glxgears` and you should see a basic 3D graphics
with rotating gears.
If both work, then I'm puzzled why 3d display in yade is broken. You
can try to upgrade to latest version from SVN, but I think that
0.12.1 was ok in this matter...
I think that you can try to reinstall packages with
restricted modules for your current kernel version.