single.php help

I have rollover images in my header and footer using js. They show up(and go to the right links) in category.php, index.php, and archive.php. But the images are bad in single.php as are their links. For example: one link in the header that goes to the root page of my site (index.html) when working correctly goes to wordpress/index.php/index.html in single.php which obviously doesn’t exist. I’m guessing the path of the actual image is also doing this. I even replaced the single.php code with the code from index.php to see if it would correct with no luck. Please help asap. Thanks!