I used a work around for the problem with flash objects displaying over thickbox.

In the thickbox.js file I added the lines:

$(“object”).hide();
$(“embed”).hide();

into the thickbox show function

and then added:

$(“object”).show();
$(“embed”).show();

into the thickbox remove function.

Because TB darkens out most of the page, if you design your right, it’s hardly noticable.

Thickbox hide objects

JavaScript