I had a bit of scare today, when after editing a page using my newly-installed JCE front-end editor, I received an anxious email from my client, telling me that part of the page had disappeared. The part in question was generated by a php include, and sure enough when I viewed the page in the back end, there was nothing between the {source} {/source} tags.
I reinstated the missing code, saved the page, and opened it again in the front end editor, and once again there was nothing between the {source} {/source} tags.
Looking in this forum, and in the Troubleshooting area, I found the answer - I needed to use
[[?php ... ?]]
rather than
<?php ... ?>
Just posting this note to remind people that if they encounter a similar problem, they'll need to do what I've just been doing, and go through their site changing all the relevant brackets.