Is the pp-checker.php even being called? Turn on logging (make sure the log location is a non-public location). You can also check your Apache access logs to see if the script is being called from PayPal.
I'm not seeing our servers dropping any requests.
Check the error logs on your servers to see if apache has any "error 5xx" around the time these orders are placed. (500-series errors are internal server errors). Also check you php logs to see if there is any fatal errors in the script.