I'm sorry to reply so late, and in another thread, but I was knee deep in a project.
I'm still having this issue, even with the raw code you offer on github.
Anytime there is a second meta box on the page, it just doesn't render correctly.
I'm not sure if this is a conflict with my theme, as in my local environment, I deactivated all plugins that weren't metabox related, and used the default 2015 theme, and this problem is still persisting.
Would it help if you had access to my remote environment?
I know you're not able to replicate this problem on your end, perhaps if you could see it on my end it may assist you.
I can email you the password privately.
Thanks for your support, this plugin has been great, but this issue is rough. I could try and use a simple text area field instead of a WYSIWYG, but I would lose the formatting options, which I would rather not lose.