How about using locate_template() for the inclusion and wp_enqueue_script() for the scripts? There’s also content_url() to target /wp-content/.
Also: How did you inspect it? Sourcecode? FireBug? Try to open source in FF and then click the link. If you get a “file not found”, you know what it’s about, else it should be loaded. The fact that it really doesn’t get “printed” to the screen is something I never saw before (in the way) you described. Best solution would be the first paragraph of my A: Switch method of inclusion and stop worrying 🙂