<?php replaced with <!--?php I am upgrading Drupal 6.26 to Drupal 7. I had a small handful of nodes (a dozen or so) that contained PHP code. After the upgrade, I've found that the &lt;?php tags have been replaced with &lt;!--?php.

I searched the Google but all I found was http://drupal.org/node/1403918. I'm not using the WYSIWYG module though. I am using CKeditor so I followed the advice in post 1 but that didn't resolve the problem.

I have the PHP filter module enabled.

When I try to edit the node, the &lt;?php tags are not HTML comments so I can't fix it that way. How can I fix this?

Edit 1: I don't think CKeditor has anything to do with this actually. I've completed disabled the CKeditor module and I'm still getting issues mentioned above.

Edit 2: I have a script that resets it back to 6.26. When I re-upgraded, the PHP scripts execute before I enable any non-Core modules. I then enabled everything but CKeditor and it fails so I don't think its CKeditor but another module. I will attempt to further diagnose.
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