We had the same issue – some of our custom post types, added through plugins, were being selected fine, but the ones that were part of our theme’s functions file wouldn’t stay selected.
We got around this by re-registering the custom post types in the functions file of the wpTouch theme we’re using. It’s not ideal as it’s prone to being overwritten by an update, but hopefully if BraveNewCode can now replicate the issue, they can get it fixed.
