What I left uncommented:
I tried to integrate the js page in xowiki like stated here http://alice.wu-wien.ac.at:8000/xowiki-doc/#file-swf but had no luck.
Well, this can't work as expected because shadowbox environment needs to be initialised once the DOM structure of a page has materialised in the browser. Upon this, an event is fired which needs to be sensed and make shadowbox to initialise. This kind of event subscription could be achieved through embedding [[shadowbox.js]], although. More critical is that the shadowbox distribution contains more than the core js script (adapters, images etc.). so all these need to be in place ...
