I ran a Network Update today from Network -> Update Network, and since then all the sites, and all the links to sites within my Admin area reference the same domain. The domain it uses is relative to the domain I've logged into.
In one example I logged into my primary domain, and now WP thinks all sites have the name and URL. If I log into another site within my multi-site installation it'll use that one.
I can't navigate to my sites using the admin area. The site's themselves seem untouched. I'm running 3.5.1, but this change occurred in 3.5.0.
I tried to post an image, but I didn't have enough reputation points.