I have been playing with the JavaScript calls from PanoTour and it seems the tour must be uploaded to a web server before the javascript starts working as expected.
I added a couple of hotspots to a scene and added a JavaScript function call like this... LaunchColorBox(http://full-url-of-file.com/,title);
and then added a javascript function to page containing tour with same structure
function LaunchColorbox(url, caption){
$.colorbox({href:url, title:caption, width:"60%", height:"55%",opacity: 0.3, iframe:true});
}
See following page source for further details of how I call/integration: view-source:http://www.panoramus.co.uk/panos/arrowsmith/gallery/
Hope this helps, as not well documented.