On Sunday night, the sites were not running the latest versions of the software and theme. As of yesterday afternoon, they were (and are).
commonsinabox.org runs the Commons In A Box default theme, as does the demo site. The demo site configuration is pretty much stock (with a few tweaks); the configuration at commonsinabox.org is modified (for instance, to have a static front page, and to have a custom menu).
I'm not sure what Bowe means in that thread. For one thing, the theme itself is still, technically, "beta". For another, the responsive menu is indeed working on the commonsinabox.org site. So, I'm not sure what to make of it.
For a number of boring technical reasons, it may not always be the case that commonsinabox.org and demo.commonsinabox.org are running the bleeding edge version of all the Commons In A Box software. Generally, this fact will be imperceptible to a user on the front-end of the site. When changes take place to the theme that are significant, I'll try to update at least the demo site right away. And if you ever notice any specific instance of something on one of these two sites not matching up with the latest stable release of the theme or plugin that is making a difference to user experience, let me know and I'll rectify it.