I just updated our source code repository and our demo site to CKeditor 4.4.1. Previously we were using a 3rd party onchange plugin but there was an onchange event added directly to the editor in recent versions so now I've removed the onchange plugin and removed the line that was removing the magic line plugin and onchange seems to work ok.
Can you try it on our demo site now and see if you think the table problem is fixed or not?
If it is fixed, then you could grab the /ClientScript/ckeditor441 folder and the ckeditor-mojoconfig.js file from our repository and deploy it to your installation then change the setting in Web.config to point to the new version of the editor.
<add key="CKEditor:BasePath" value="~/ClientScript/ckeditor441/"/>