OK, this one is really strange and I cannot explain it at all. Just to set up the environment, I'm using ASP.NET 2.0 and the latest version of FCKEditor (2.4.3) running on IIS6 (Windows 2003 SP2).
I have built a CMS system for a bunch of web sites. Its a little complicated but I will hopefully be able to explain it. I have one folder that multiple domains are assigned to in IIS. That folder has inside it the code for the web site, CMS, FCKEditor, etc. Also the folder for the userfiles are all located in a folder named uploads. Inside that folder uploads is a folder for each web site. Inside the code it looks at the domain name and then determines which web site it is and assigns the users to the correct folder inside of uploads.
Here is what it looks like:
/root /bin /fckeditor /uploads /site1 /site2