Sounds like the form is not submitting properly, and just keeps using the old values. As a temporary fix, you can either:
- Debug the module's PHP code and fix the form submission yourself
- Or look in the database and manually make the necessary changes to the configuration (might be in the
variable
table or in a custom table created by the module itself)
As a more permanent solution, I'd file a bug in the module issue queue for the module you're using to integrate CKEditor on your site. If you tell us what version of Drupal and what module (and its version) you're using to integrate CKEditor with Drupal, someone here might be able to debug the code as well.