The way it was explained to Joel Spolsky in the article linked earlier is that Gates just pokes away at increasingly fine details until he finds some question you can't answer, and uses that to make you look dumb. Its actually just a form of intellectual bullying, like a jock who challenges you to an arm wrestling contest before he'll let you out of the changing room.

Thats not to say that Gates isn't extremely intelligent and hardworking, just that his approach isn't necessarily the best. Also, Spolsky's anecdote is from a few decades ago. Gates will have matured a bit since then.