It took me quite a while to figure this out, so here is a solution for anyone who finds it useful :)

If you are running Jquery in noConflict mode, the Thickbox script will not work anymore. Now, there are two solutions.. I'll leave it up to you which you like best.

The first is to place this in your head section:

(function($) {
$(function() {
// content of Thickbox script
});
})(jQuery);

Another solution is, to open the uncompressed version of Thickbox, and to replace all occurrences of $ with jQuery or the prefix you are using.
Then you will be able to use the normal functionality of Thickbox..

It will take up a bit more space though...