CKEditor 4.1 introduces a new option "Advance content filter".
This makes adding media fail

===> https://drupal.org/project/ckeditor

Note for CKEditor 4.1+ users
If you are using CKEditor 4.1+, you should adjust Advanced Content Filter settings. If you have any trouble implementing this feature, you can turn it off by setting:

config.allowedContent = true;

in the Custom JavaScript configuration field of the Advanced Options setion for your CKEditor profiles.