Custom menu problem

I’m having a custom menu problem. I’m writing a theme that has 3 custom menus. In two of them, most of the menu items I add link to the home page, no matter what I tell them to link to. I got one page link to go to the correct page, but I can’t get another one to work. When I look at the menu items in the admin area, they are all correct, and all have the right URLs. But when I look at the links on the site, they all (except one) point to the home page.

You can see the problem in action here:
http://white.alchemycs.com/2011/09/atomicwar0107-2/

I’ve Googled, and haven’t found anyone else with a similar problem. I’ve updated my permalinks just in case, and that didn’t help.

Any other suggestions?