With a bit more tinkering I think I found the "problem". While setting up the new 802.11ac Airport, I let the setup software copy the configuration from the 5th Gen Airport that it was replacing. As a result, it configured itself to only use 20MHz channels for the 5 GHz network.
I reset the Airport to the default setup, with no other Airport to copy, it let me set all the config options maunally, and now uses 80 MHz wide channels for the 5 GHz network - giving me a max rate of 1300 Mbps.
The lesson here is - don't let the setup software copy an existing configuration if you want to take advantage of the new features. Seems like a bug in the setup software to me.