I've never seen SSI used with PHP in this way so this is something of a long shot, but can you try changing:
AddOutputFilter INCLUDES .php
to:
AddOutputFilterByType INCLUDES text/html
the reason it's not working is that your files no longer have a .php extension (or any extension), since you're routing everything through index.php. The change I've suggested will filter all text/html output (which should include PHP) though the SSI parser, instead of doing so by extension.
Tim Fountain
2010-08-16 17:51:19