Hello,
in the current version you added som DNS checks using the A or CNAME record.
Currently letsencrypt is not able to process ipv6 only webpages (which I am waiting for). But at their upcoming features page, the ETA for ipv6 is before 31.08.2016 (https://letsencrypt.org/upcoming-features/). Can you please check if the letsencrypt plugin is ipv6 compatible (using AAAA records)?