I am currently having issues with PayPal communicating with our website and CiviCRM. Half of the recurring contributions have not shown up over the past couple months and every one-time donation has listed as "Pending/Incomplete Transaction over the past week. Our current version of Civi is 4.4.3. We have checked the URLs and our web host has white-listed all IPN's even though they don't think anything was being blocked. We have also applied a few patches of code from newer versions and we are still having issues. Is anyone else having this problem. This is a bit out of the scope of my knowledge. Thanks.
Does Paypal insist on an SSL certificate? Maybe yours is not compliant?
Did you configure IPN link correctly in your paypal accunt? Also you need to configure it in your server configuration file.