One of the first things I usually need to do when installing a new Drupal site, is to change the settings in the new (version>4) CKEditor so that I can type classes and ids and not have them strip out.
To do this, do the following:
- Go to Configuration -> CKEditor -> Full profile (or admin/config/content/ckeditor/edit/Full) or other profile that you use
config.allowedContent = true;
This is caused by the new Advanced Content Filter in CKEditor 4.