Backward Compatibility problem

I have set up multiple ipn and there seem to be no problem with new signups. But the old ones are not getting renewed. I have uploaded supporter-paypal.php to root of my install (upgraded from supporter plugin). But when i checked my ipn history in paypal, they seem to be sending ipn to subsite.mydomain.com/supporter-paypal.php instead of mydomain.com/supporter-paypal.php.

EDIT: Just to add, there is no log in my ipn forwarder folder to show that ipn was actually received, eventhough it was sent by paypal