I'm assuming that you all don't wish to call the header so that objects like navigation, logo, etc. don't appear inside your light-box correct?
If so, creating a separate header for your single.php or even a certain category, page, etc. would be an easy solution - one that doesn't print out the information you wish not to be displayed.
Some of these links could give you the answers you need. Give this a look: http://wordpress.org/extend/plugins/dynamic-headers/ I have never tried this plug-in but it certainly could achieve your desired results.
Additionally, another alternative could be using conditionals inside your header.php file itself using categories to chose which posts are displayed in light-boxes. Something like this:
<?php include(TEMPLATEPATH.'/headercontact.php'); ?>
<?php include(TEMPLATEPATH.'/headerdefault.php'); ?>
Again, never tried these before but they should work.
Hope this helps!