Nav Buttons Disappear with Permalinks

I made a site with a static, image-based navigation bar. It has javascript rollovers. I know this is not preferable but I was using a strange font for the navigation.

Anyway, the navbar worked perfectly but when I turned on pretty permalinks the navbar disappeared. I gave up so I am not using permalinks now. The question is…why? The navbar is at the very top of the index.php and page.php files. I can’t remember why I didn’t put it in the header but it seemed like the thing to do at the time.

I really would like to use permalinks but it’s a mystery why the static navbar disappears. Any ideas?

Thanks!!!