IIRC in ZC1.3.7 the PayPal IPN Handler uses its own application_top.php file which does not load any of the auto loaders so user defined notifiers and classes will not get loaded. ZC1.3.8 uses the standard application_top so autoloaders should get loaded. I don't recall ipn_main_handler.php triggering any notifiers at the point of order creation or status update though.
The last time I had to hook into the order creation process I ended up just changing the includes/classes/order.php file. It meant changing a core file but it ensured that all orders were caught and everything was simpler.
Regards,
Christian.
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