It means that for some reason PayPal is getting something other than a 200 OK response back from your script. If it looks like your script is working it could mean that all of the tasks are completing, but then an issue at the very end causes a failure that you don't even see other than the fact that PayPal isn't getting a good response back.
You need to check your web server logs for the times when your IPN script was hit and look at the results. You'll probably find a bunch of them that show 500 or something other than 200. You should also be able to see the error details there, too, and get it resolved.