Multisite planning trouble

Hello, I admin a whole lot of varied web sites, on varied systems, under the umbrella of https://www.birds.cornell.edu and I want to add WordPress to the mix. So far it’s gone well but I’m having trouble integrating a new site into the topology and I could use some help and advice.

I have WP 3.1.3 running as a network, and it’s on the same server as a number of other sites, but running on its own IP. Since we don’t want WP to serve our home page, I have got WP installed so that the root is named https://www.birds.cornell.edu but it doesn’t really live at that address; traffic gets routed to the various WP blogs through IIS proxying rewrites. This works well, and appears seamless so it looks like the blogs are living under the proper address. I also have a non-public service address https://www.ornithopolis.org mapped to the IP that WP is using, so I can bypass the rewrites if necessary. I also have WordPress MU Domain Mapping installed, but I haven’t tried to use it until today

Today, we wanted to launch a new project, content.yardmap.org and point it to a blog running on https://www.ornithopolis.org under a MU domain mapping. I set this up on a test server and it works just fine: supertest.yardmap.org really lives at test.ornithopolis.org and it works seamlessly. However when I tried to set this up on the live server, I got a 404 error. Somehow, the configuration that includes the mapping to https://www.birds.cornell.edu (which is unrelated to this blog, but necessary to other blogs on the network) is causing it to get confused. Any suggestions on how I can untangle this?