Inconsistent Results with Multiple Domains

I’ve been using Certbot for years on my domains discchord.com and appkaiju.com. Today I’m launching another site on the same webserver and I’m running into a bizarre error.

If I do:
sudo certbot certonly -d discchord.com -d www.discchord.com -d appkaiju.com -d www.appkaiju.com -d gnubesoft.com -d www.gnubesoft.com --dry-run

Everything works as expected:
http-01 challenge for appkaiju.com
http-01 challenge for discchord.com
http-01 challenge for gnubesoft.com
http-01 challenge for www.appkaiju.com
http-01 challenge for www.discchord.com
http-01 challenge for www.gnubesoft.com
Waiting for verification…
Cleaning up challenges

However, as soon as I run it without the --dry-run it will only renew the existing domains. It is inconsistent about that too! The first time I tried it renewed www.discchord.com discchord.com appkaiju.com … the second time it just renewed appkaiju.com. On none of the attempts did it ever make it to gnubesoft.com. I’m selecting (E) for Expand when asked.

What am I doing wrong? I seem to be on a time-limit for how many times I can run this in 7 days and I’ve already burned 2 attempts.

Thank you very much for any help you can provide! I am so grateful to Let’s Encrypt for this service!


My web server is (include version): Nginx (latest)

The operating system my web server runs on is (include version): Ubuntu 16.04

My hosting provider, if applicable, is: Self

I can login to a root shell on my machine (yes or no, or I don’t know): Yes

I’m using a control panel to manage my site (no, or provide the name and version of the control panel): no

The version of my client is (e.g. output of certbot --version or certbot-auto --version if you’re using Certbot): certbot 0.31.0