Adds friendly permalink support, template files, and a new conditional for public, non-hierarchical custom post types.
First, make certain the custom post type is supported by the plug-in. This plug-in will only add archive permalink for non-hierarchical, public custom post types that have a "slug." There's plenty of documentation on register_post_type if you need help verifying that.
If you're certain it's a supported post type archive, try going to Settings > Permalinks, and just hit "save" to refresh the permalink settings and cache.
If that doesn't work, try getting in touch on our support page.
Manually. Any number of ways, like a "Custom Links" menu item using the new nav menus, manually adding a link in your theme, or (if you're clever) even fetching the post type objects that meet the requirements using some API jujitsu.
I'm going to try and add a new meta box to the "Menus" manager that allows easy adding of custom post types. I got about 75% of the way there already, but there's a lot going on in that API that I still have to wrap my head around!
In the mean time, consider using the body class as a work around.