Under edit, preferences, code rewriting - there is a line which is checked (and greyed out), never rewrite code in files with extensions, and php is part of the extensions; code should never be rewritten, but it has happened to me. I opened a page and as it opened it was changed and needed to be saved. When I looked at it I saw that PHP code had been changed and no longer worked. I changed it back and it was fine.
Further down another line is also checked, encode <, >, &, and " in attribute values using & - that's the one I'm wondering if I should uncheck it - I like it but it should only convert these characters when I paste them in the WYSIWYG window.
Lastly, I have an exclamation point next to the Universal Email in the server behaviors - this is the registration solution package, the users_Registration.php page, and the server behavior panel has the exclamation point and then UniversaL Email 1 (mail) [prior version]