Sorry, I forgot to close the loop on this thread.
The problem for me was really in my understanding of how the email updates worked. I'm not sure why, but I was expecting FeedBurner to poll my blog more frequently (say, every 30 or 60 minutes) and send emails whenever it sees updates. However, as Matti pointed out, it only looks at your feed once per day during a configured 2h window. I think the UI could make this clearer but either way things are WAI.
I picked a more appropriate update window and the mails are flowing as they should be. Thanks for the help!