document.domain setting

I am trying to use a custom file manager in the same domain, but different subdomain in conjunction with fckeditor. I can get the filemanager to work properly and open from the fckeditor dialog windows, however trying to call setURL in the fck dialog window causes the permission denied error.

I did some research and found that you can set document.domain in both the dialog and the filemanger document to be the root level domain and yes that works, however it causes errors within the dialog window. I assumed the fckeditor does some tricky things and sets its own document.domain property somewhere, but searching all the source files reveals no instance of the word domain anywhere.

Has anyone else successfully found a work around or knows how/where document.domain can be set?

Any help is appreciated.