I was kind of surprised that CKEditor does not work with ASP.NET bundling in optimization mode. Faced some path related glitches.

Turned out there is some additional acrobatics with CKEDITOR_BASEPATH required:

<script type="text/javascript">  
    CKEDITOR_BASEPATH = "@Url.Content("~/Scripts/ckeditor/")";
</script>  

Thanks to this post http://stackoverflow.com/questions/24503284/ckeditor-not-working-when-site-is-deployed-on-iis

Hope it helps.