I had the exact same problem (on nVidia FX 5700) connected with Synaptic displaying very few packages (about 1100 total). That made me take a look at System -> Administration -> Software Sources and it turn out that all the repos were disabled there. I have no idea why they were disabled (maybe because i had no internet connection during installation) but the point is that enabling them solved the problem and the Appearence -> Visual Effects nicely installed the drivers automaticaly then.
I had the exact same problem (on nVidia FX 5700) connected with Synaptic displaying very few packages (about 1100 total). That made me take a look at System -> Administration -> Software Sources and it turn out that all the repos were disabled there. I have no idea why they were disabled (maybe because i had no internet connection during installation) but the point is that enabling them solved the problem and the Appearence -> Visual Effects nicely installed the drivers automaticaly then.