hi james,
I have created a few BDs using the manual assignment and it worked well over here.
are you sure, you turned off the auto-routing?
according to seamless playback of menus I could say that menus for BD were created in a different way, as jon mentioned before.
the IG (interactive)-stream, is the stream that containing the informations that you know as button-overlay within DVD. it is much more complex than button-overlay and can have in/out-effects as well, but this can´t be done with encore.
creating IG-streams (or better graphics for it) is a lot work, much more than creating a button-overlay for DVD.
maybe there will be a FULL mac-BD-authoring-system in future! rivergate software is working on it.
cheers
danny