I'm having a similar problem.
I just made this track:
http://tm.mania-exchange.com/s/tr/73674
in the multi-env pack. It's a pure valley map (valley env and valley car), but doesn't show up in the map listing in the valley pack. I can load it in the valley editor, and re-save, but it still doesn't show up. Has this always been the case? It seems like I've made "pure" maps in the multi-env pack before, and they've just worked?
I *really* don't want to have to re-validate in Valley, since it took me about four hours to make a no-respawn run the first time.
Is there some way to fix this?