I just figured out how to fix the PayPal Instant Payment Notification Warning message. Here is what I had to do, in case anyone else is getting this error.

When I moved my site, the primary domain was changed. For some reason, I was using this instead of my subdomain name within the PayPal settings. So I just updated that.

The hardest thing was to figure out where to do this. Turns out, the Instant Payment Notification (IPN) settings are found under My Profile-->My Selling Tools-->Instant Payment Notifications. Click the link Update then click Edit Settings and change the Notification URL to match the path where the file resides that is called: ipn_main_handler.php