I think the first issue is your use of trying to include a home link, and wp_page_menu
I'm not totally sure, as I haven't messed with the new menu system a lot....but I no longer include a home in with wp_nav_menu
The point of the new menu system is so the user can create flexible menus. So the user is able to add their own home tab. No need to code it in like you've done......
I tend to steal a lot of code from default WP themes when I'm learning stuff..... in the twentyten theme, functions.php, there is a snippet of code that will add a home tab to the nav menu when the default page menu is used (ie, if no custom menu is set up)
I think if you deal with the home tab issue, that will get everything on one line, then we would be able to check out alignment a bit better
Also, I don't think you need to wrap the whole menu in
<ul> as that happens automatically....
<?php wp_nav_menu( array( 'container_class' => 'menu-header', 'theme_location' => 'primary' ) ); ?>
for instance here is my menu code (wrapped in a nav div like yours) but that's all I have, taken from twentyten theme, it automatically outputs appropriate