FCKeditor on a media server

We have a situation that we can't seem to find an answer to.
We have multiple applications that are hosted at subdomains (IE app1.mydomain.com, app2.mydomain.com, etc). We recently set up a central "media" repository for all of these apps to pull from at media.mydomain.com, this domain is served by a bare bones http server that is just serving static content, so its fast. However, we cannot seem to get FCKeditor to work in this scenario. There are a bunch of javascript errors, some say "permission denied" so I assume this is a cross site scripting issue.

Is this setup just not supported by FCKeditor? And if not, why not? This is a pretty common optimization technique that is highly recommended by just about every major web framework I've used.