Just had a bit more experimentation on a blog (on a different server) that had menus from 3.0 and I upgraded it to 3.0.1 and now I can’t change the menus.
It has 2 menus that were both working before and I could change what menu was used fine.
However today I upgraded, added a new menu called test with a test element and tried changing both of the menu positions to use this new test menu and neither of them changed.
So I think the problem is not that it is always using the default menu, but that the menu’s seem to no longer change.
I can even edit the old menu’s that should not be showing anymore and add new elements and it will show the new elements on the page.