I use JCE many years an since 2 or 3 versions there is a bug in the editor.
If I open an article and the tab is "code" then I have the correct syntax for "php start" and "php end" picture jce_11.jpg
afterwards I switch the tab to "Editor" and back to "code" then JCE change the code inside the i-frame - definition picture JCE_12.jpg
Best regards
Peter