Using Seperate FCKConfig on main domain and subdomain

I am trying to use FCKeditor (.NET) on a subdomain which is setup as a completely seperate website in IIS. All the JS files are on the subdomain and the .dll is in the bind folder.

The main (www.) site also has the .dll file in the bin folder and all the fckeditor JS files.

On the subdomain, I set the basehref of the editor to the subdomain (http://sub.domain.com), but when I try and use a toolbarset from my fckconfig.js file (http://sub.domain.com/fckeditor/") it says it can't find it. If I use one of the toolbarset names from the www. site (http://www.domain.com/fckeditor/") it works.

However, if I include the toolbarset from the subdomain into the www fckconfig file, it still won't work on the subdomain.

I also have a similar problem with the editorcss file which isn't setting the bodycss correctly.

If I remove the fckconfig file from the subdomain folder the editor still works.

Any ideas how I can just get it to use all the files from the subdomain fckeditor folder?