drupal strips javascript

Issue Summary

Hi,
sorry if this is the wrong place but I am having problems with nodes being loaded into colorbox with a colorbox-standard class on the link, the problem being the node--type.tpl file I am using contains some javascript inside tags - the overlay is correctly displaying the node using this template but any javascript is being stripped out.
I understand this might be standard behaviour to avoid XSS etc but is there a way I can get my javascript inside the node?
Ive tried with drupal_add_js with no luck - it needs to be js that runs not attached to a link etc.

cheers!