I have just upgraded from 4.1 to 4.3. The config file is the same. However, now, when you go from WYSIWYG to source view, a new blank paragraph is added to the top of code fragment.
This only happens in Firefox v.25.0.1 Mac. I tested Safari and Chrome and they were okay ... not sure about PC versions.

gloney, that's a quite old
gloney, that's a quite old error. I struggle with that since CKEditor 3.x and Firefox on Windows, Linux and MacOS.
By the time searching for a solution I didn't find any of use, so I developed my approach around it by processing the data before saving by removing the unwanted blanks with regex/replace (preg_replace in php). Works great so far. The only drawback is that you will have to assign a special class to empty paragraphs you don't want to be removed...
version 4.1 to 4.3 problem
This is not a problem in version 4.1 on Firefox. When I upgraded to 4.3 it started happening. So I returned to version 4.1 and the problem went away. No change to Firefox.
Could you attach HTML for
Could you attach HTML for which it happens and your configuration?
Piotrek (Reinmar) Koszuliński
CKEditor JavaScript Developer
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Attached examples
I have attached the html and config files
Attachments: