There is something strange going on at the moment, though, but not sure it has to do with DNS. I actually tried set up my first cert about 10 hours ago with Let's Encrypt, and got a variety of ungraceful errors with the same configuration. Only one was related to DNS. Most were code 500 from the api servers.
April 14, 2016 12:47PM MDT
April 14, 2016 6:47PM UTC
[Investigating] We have noticed an increased number of errors. We are investigating now.
April 14, 2016 1:21PM MDT
April 14, 2016 7:21PM UTC
[Resolved] Systems have fully recovered and all services appear to be operating nominally. Cause seems to have been a transient hardware failure and further investigation is under way.