Not sure if it's related, but PayPal IPN is no longer working for me. I have changed no PayPal settings. I did recently upgrade to 5.0.3, and haven't had a successful IPN applied yet. I have logged into PayPal, and used the IPN History page to resubmit the IPNs that didn't post. They claim to succeed, and PayPal is most definitely posting the IPN back to my web server:
173.0.81.1 - - [14/Jun/2012:10:54:45 -0400] "POST /modules/gateways/callback/paypal.php HTTP/1.0" 200 0 "-" "-"
173.0.81.1 - - [14/Jun/2012:11:51:33 -0400] "POST /modules/gateways/callback/paypal.php HTTP/1.0" 200 0 "-" "-"
Those two log entries correspond exactly to the PayPal IPN history of when they send the IPNs to my server. The information shown in the IPN on PayPal site looks correct. Yet the payments do not get applied in WHMCS.