A quick post-script on this -- so that we have the solution recorded for the next person who runs a search on BF.

While there are in fact minute differences between the pre-2001 Campy 9-speed shifters and the post-2001 Campy 9-speed shifters, that wasn't the problem. In fact, according to this article from Sheldon Brown and an even better one from CTC here, they are compatible. The jockey pulley has enough play to cover the small differences in cog spacing.

The problem turned out to be a mis-placement of the cable-fixing bolt. I had it rotated out of position, so the cable was not routed straight through it. Therefore, as the lower half of the rear derailleur pivoted out, the cable was being pulled at a different angle, with a slightly greater radius. Hence, perfect shifting in the smaller cogs, poor shifting in the larger cogs.

Moral of the story: be sure to route the cable through the little groove in the cable-fixing bolt when you set up your RD.

Andrew