Even we have sporadically encountered this problem - but only on local machines running Wampserver and never on hosted stacks (hence this issue was not considered critical).
Could you please try out the following and let me know if this rectifies the problem?
1. Go to 'includes/ckeditor' folder within your Couch installation folder.
2. Remove the following three files from the folder - ckeditor.js, ckeditor_php4.php and ckeditor_php5.php.
3. Place the three patched files I am attaching with this post in place of the removed files (we are replacing the ckeditor.js file with a PHP file named ckeditor_v35.php).
Please let us know if this solves the issue.