Is the latest version of the CKEditor code supported with CKEditor 6.x-1.13 (Drupal Code 6.26)? I upgraded CKEditor on my test system, installing it to sites/all/libraries. Initially, the rich-text editing field did not show up at all. When I checked the CKEditor configuration, it indicated that the 'kama' skin and the 'tableresize' plugin were not found. It looks like just going into the CKEditor configuration caused the rich-text edit field to show up but only a limited set of buttons are available and they are a rather drab grey. All the 3.6.3 buttons appear in the CKEditor profile configurations.
http://drupal.org/node/1851606 suggests success using the dev version. However, it looks like the author of this issue decided to revert back to 3.6.3. I checked the link to the dev changelog but the link appears to be broken.
I have attached screenshots of the 4.0.1 and 3.6.3 toolbars.