How to debug PayPal IPN issue?
I kept pulling my hair out until we migrated to paypal pro (with it's own set of issues :)) but a couple of things to look at:


Check apache error log,
Paypal has a log that shows details of all IPN calls to server.
Make sure you have correct URL for http vs. https
Check civicrm log files in files/civicrm/ConfigandLog
Make sure firewall rules (and especially modsecurity) are letting things post
Don't know about joomla but in drupal, I always need to disable IDS (Intrusion Detection) for anon users and it often triggers false positives.