<?php replaced with <!--?php
You don't have to accept this as an answer, but I would recommend not using CKEditor with the PHP input format. In D7's CKEditor module you're able to attach CKEditor to input formats, as opposed to D6 where you specified textfield IDs and paths and such. Therefore, you can just attach CKEditor to the "Filtered HTML" and "Full HTML" input formats and leave PHP alone. I just think it's a bad idea to try and use wysiwyg formatting that contains code like this.

So, my recommendation would be:
1) Disable CKEditor for the PHP input format.
2) Edit the handful of nodes and replace &lt;!--?php with &lt;?php