Advanced CSS/JS Aggregation breaks older versions of CKEditor

I have a site where I am using CKEditor with the CKEditor 4.0.1.
Advanced CSS/JS Aggregation breaks the CKEditor.

To try to remedy the situation I go to the JS Compression settings page where I disable js compression on all of the CKEditor js files:
- sites/all/modules/ckeditor/ckeditor.config.js
- sites/all/modules/ckeditor/includes/ckeditor.admin.js
- sites/all/modules/ckeditor/includes/ckeditor.utils.js
- sites/all/modules/ckeditor/includes/jqueryUI/jquery-ui.min.js
- sites/all/modules/ckeditor/includes/jqueryUI/jquery.ui.sortable.min.js
- sites/all/modules/ckeditor/includes/jqueryUI/jquery.ui.widget.min.js
- sites/all/modules/ckeditor/includes/jqueryUI/sort.js

It still does not work.
To get CKEditor working again I turn off a big chunk of the module's functionality.
- (off) AdvAgg Bundler
- (on) AdvAgg CDN CSS
- (on) AdvAgg CDN Javascript
- (on) AdvAgg Compress CSS
- (off) AdvAgg Compress Javascript
- (off) AdvAgg Modifier
- (on) Advanced CSS/JS Aggregation

On another site I am using CKEditor with CKEditor 4.1.2
It all works.

I go to the JS Compression settings page. There is only 1 CKEditor js file.
- sites/all/modules/ckeditor/includes/ckeditor.utils.js
The js is obviously a lot simpler.

Is there a way to make Advanced CSS/JS Aggregation work with the older CKEditor 4.0.1?
I do not want to upgrade the problem site to CKEditor 4.1.2 because of other issues.

This module is awesome, but CKEditor has some pretty complex js and is not hard to break.
Thanks