Ok, so we have an interesting setup using WordPress 3.1 (multi-site).
Originally we had a service with the domain blogs.domain.edu (which is actually a cname to blogs.server.domain.edu). We have decided that we want to rebrand it as sites.domain.edu, but still having blogs.domain.edu answer. So blogs.domain.edu/user and sites.domain.edu/user both point to the same thing.
To make things even more complicated, we do indeed have the Domain Mapper plugin installed as well.