CKEditor 3.3 - Cannot set configuration settings in config.js

I am using Drupal 6.17 with the WYSIWYG and CKFINDER modules. I have a multi site drupal environment set up with several sites.

I am trying to set the BodyId and BodyClass of the editor so I can set the base font, background color etc of the html in the editor window. I am also trying to change the stylesheet so my classes are reflected in the STYLES dropdown. I don't think the editor is seeing my theme's stylesheet at all.

I've tried changing the config.js file in the CKEditor base directory (as specified in the Tips and Tricks node) and I've tried moving that file to my theme's base directory. I've tried renaming it to ckeditor.config.js. I've tried adding the code to set config attributes in another javascript file. I am pretty much out of ideas.

This is not working like any of the existing documentation talks about.

Any help would be very much appreciated.

Thanks.

get the styles dropdown to work properly and