I ran into this issue, forgot about this thread, went through LetsEncrypt's threads and their solution for this problem led me... here! Very nice.
Just did the exact same thing. Let'sEncrypt forum had the link which led me here right about the time @JaredBusch was responding in my other thread.
It has been posted on here more than one time. I should probably find one of those posts and make @scottalanmiller tag it appropriately.
Edit: Or too slow..