Well, I figured out a hack-around for it anyway... a wrinkle is that the nav class isn't named by the page slug as it probably should be... instead it's given as "qa-nav-main-custom-#" where # is the number of the custom page in the admin. The hack was to add the following to my page's page template:
$qa_content['navigation']['main']['custom-2']['selected'] = true;
(my page is the second custom page, I guess)
This gives the following code for the Badges page:
<li class="qa-nav-main-item qa-nav-main-custom-2">
<a class="qa-nav-main-link qa-nav-main-selected" href="./badges">Badges</a>
and voila, the nav item is selected :)
Hopefully I can dig deeper and find out where to add a check to the main code, or at least change the "custom-2" to "badges" so I can just write a command for it, but maybe Gideon can help?