Currently the CKEditor is used as WYSIWYG editor. It is improvement over previously used FCKEditor, but it has one major downside: for security concerns it removes HTML tags and HTML tag attributes, that can't be specified using any of used CKEditor plugins. The feature is called Advanced Content Filtering - http://docs.ckeditor.com/#!/guide/dev_acf.
Proposing to disable Advanced Content Filtering to allow administrators enter website content as their see fit. This is more user friendly approach, then figuring out what should be additionally allowed on each In-Portal based project.
Add "CKEDITOR.config.allowedContent = true;" to the end of CKEditor configuration file (default Admin Console config and one used by Simple interface preset).