I have just switched from using interbrite's letsencrypt-vesta to the newly integrated Let's Encrypt system.
Quite a tedious process, going through all domains manually, deselecting SSL Support, saving it (required to not get a "not found" error), then selecting SSL Support and Lets Encrypt support and saving it again. However, all SSLs have been converted and are working fine.. except for one single domain which upon saving gives the following error: "Error: LE x.y.com validation" (where x.y is subdomain.domain). It is running just fine with the DNS set just like any other domain, and it used to work well with Let's Encrypt via interbrite's letencrypt-vesta so something must be wrong here:
Also, default.domain, which contains a self-signed SSL (basically just a catch-all in case someone connects through https to the server's IP address or a wrong subdomain), shows SSL Support: Lets Encrypt, without Lets Encrypt Support even being checked (this wouldn't even be possible given I don't own the actual domain). I even tried to reset the SSL, deleting it and putting it back in, but the mistake persists: