custom nav menu disappears from home/index page when set to default menu in 2010

My custom navigation menu disappears from my home page when i set the Primary Menu to my custom menu in wp 2010 theme. The menu appears on every other page except for the home/index page.

I’m using custom post types and a custom taxonomy that i’ve made my custom nav menu out of. The menu works fine on posts, pages, and everything else just not the main index/home page.