It's really difficult to get any script working with Wordpress. Which is why they have plug-ins. WP just really seems to mess with paths making using a relative path near impossible. Which means you have to find every instance in the script (or scrpts) where it uses a relative path and change it to absolute.
But there are a number of good plug-ins to do what your trying to do. Maybe not quite as pretty as light box (although there is a light box plug-in). I tend to google them rather than go through the plug-in finder on the WP site or search using the function inside your WP install.
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