After a lot of searching on google - I ran into the documentation of the fckeditor on www.fckeditor.org. Here everything started to clear up.
in the mambot file fckeditor.php I replaced the line:
oFCKeditor.BasePath = "$mosConfig_live_site/mambots/editors/fckeditor/" ;
oFCKeditor.BasePath = "/mambots/editors/fckeditor/" ;
It seems the reference with the site included breaks everything. Now I've got a working FCKEditor integrated with my joomla installation. Tested in both firefox and ie7.
Thanks for a great alternative to TinyMCE