It Is not the card, it's the driver..
I had a laptop with nvidia card, when I changed the driver (nouveau) for the one in nvidia site, transparencies were all gone. But instead I had 3d support and decided to install compiz...
I found lots of options to play with, effects and all of that..
In your case 3d should be supported, I do not know for sure, but you can try to check it out:
glxinfo | grep direct
But for what I see, driver do not support transparencies.
Hope it helps..