After updating my Civi installation from 4.6.x to 4.6.22, my CKEditor was broken (blank screen in edit window, all areas).
After checking my js console, I found my justify plugin folder was missing:
../civicrm/packages/ckeditor/plugins/justify <= folder missing
I downloaded the plugin from here: http://ckeditor.com/addon/justify
Expand the .zip in plugins folder, it will create the justify folder and fixes the problem.
It looks to me like that plugin is not missing in the latest 4.6. But it's incorporated into the build of CKEditor, not in a separate file. Maybe you just needed to clear your caches?