I've noticed this for a long time now, and with the final release of 3.0, it has not been improved.
I've been having a huge problem with my menu (wp_nav_menu). It does not show pages in the right order, and sometimes it does. It removes all links and the whole menu whenever I add custom links, so that I always have to delete the menu and start over again.
One common thing as well is that subpages tend to become parentpages, even though that is not correct.
I'm using a replica of Twenty Ten theme (aka, just changed fonts and color etc. and have not touched the core code of the theme)