All permalinks on multi-domain site redirect to main site.

I have a client's site: http://zysites.com/silververitas/

That domain is mapped to my main site http://zysys.org

For some reason, you can access the main page of the site and any previous post pages, but you can't view posts, categories, or tags without it redirecting back.

This happend all of a sudden. DNS is using A records to point zysites.com to zysys.org. I upgraded apache recently, but I believe it was working before and after that upgrade (but that is the only that changed recently). I also upgraded to the latest version of the plugin.

What might be going on here?