I searched on Paypal and found this response is their Business Help section:

Why did I get an email with the subject "PayPal Instant Payment Notification Warning"?

You’ve received this IPN warning email because PayPal is having trouble delivering IPNs to the URL or URLs in the email.

First, check your IPN settings. Ensure that the URL is set correctly and that the IPN script is in the correct location on your server, as specified in the IPN settings on your PayPal account or in your PayPal-integrated payment processing software.

Here's how to check your PayPal account's IP history to see which IPNs are failing:

Click Account Settings.
Click Notifications under "Business Profile" on the left of the page.
Click Update beside "Instant payment notifications."
Click IPN History Page. (This appears only if you have IPN enabled.)
On the IPN History page, look for those IPNs that are in a retrying or failed state to learn which IPN script is failing. Click the Message ID for each IPN to see the message that was sent, the number of retries, and the URL that received the message.
So I did all those things and found an https response code of 200 for each transaction in the IPN history. That's supposed to mean the request succeeded. I also read through the transaction messages for several of them and do not see anything that indicates a problem. So now I am truly confused. Paypal's own records indicate that each of the recent instant payment transactions has gone through properly. I will contact Paypal customer support and report back, but I can't see any problem.