linking scripts to subpages

My site was working all right when it ran locally, but live I have a few problems I haven’t seen before. It’s probably simple, but I can’t figure it out.

all my files/pages/custom templates are located in the same folder on my server, but on some pages my scripts, from header.php, don’t work. All pages load the header (<?php get_header(); ?>), and the header is loaded, but without images and script functionality. At the same time, the scripts and images from the header work on my start-page.

does anyone recognize this issue? Now, for instance, my scripts work on all pages, except subpages and the startpage, but it all depends on how I link to them in the header.php. I can get the scripts and images to work in the startpage, but then it all stops working in the other pages. What am I doing wrong? Is it something about the hierarchy of my pages?

can i do <?php include (‘TEMPLATEPATH header.php’)?> with different locations on different pages?

can I locate my files differently?

Any help would be appreciated!
TACK!

//C