Stories like this really make the case for open source app servers for me. The breadth of functionality they offer is so wide that when something does go wrong not only is it way easier to debug the issue and find out whether your code or the application server is at fault but also once you found the issue you can actually fix it yourself.

We run a custom patch set against our application server (which we contribute upstream) and I couldn't imagine using a closed source app server. We have other teams that work with closed source app servers and they really envy us.