Apache plugin "Only one vhost per file is allowed"

I got my beta acceptance email this morning and set about trying to install the certificate using the Apache plugin. After selecting the appropriate subdomain, I get a message telling me “Only one vhost per file is allowed”. There is most definitely only one vhost in the config file, which you can see here: https://gist.github.com/Gremlyn/a67d60847cd645b4e0d0

I found the code that does this check and though my python is a little rusty, it appears that it’s actually checking the newly created copy of the vhost, which when I check looks nearly identical to the original with the exception of the nodes added.

I am sure I can install this without the plugin, but if there is some kind of bug here then it’s probably better to look into it.

I’m running an Ubuntu 14.04.3 LTS server.