domain mapping plugin and vhost setup

have a few setups that work and a few that dont, not sure why some dont.
the problem is the wpmu is setup on a virtual host, so the when we add a subdomain, then use domain mapping plugin to resolve the subdomain, it actually redirects to the root site, which is called up IP based.
not sure why some of our setups work and some do not, but is there anything that can be done to insure it works on a named site, in a virtual directory.
when I say some do not, these are separate domains on separate servers, with separate wpmu installs, not some domains on the same instance.
thanks in advance for any tips.