This may well be the reason:

http://drupal.ckeditor.com/troubleshooting#12

Ian

From: support-bounces@drupal.org [mailto:support-bounces@drupal.org] On Behalf Of Anthony
Sent: 10 April 2012 19:21
To: support@drupal.org
Subject: [support] ckeditor

I am using CKEditor but find that it is inserting a paragraph with a blank at the end of any source code I edit causing my layout to get out of whack. Does tinymce also do this?
Thanks

--

Anthony Stefan Maciejowski