I'm unsure as to the construct of the page but the following code should fix it with a little tweaking
$(document).ready(function(){
$('.element').click(function(){
$('.body').css({'overflow':'hidden'});
});
$('.overlay, .close-button').click(function(){
$('body').css({'overflow':'visible'});
});
});
Just replace the following with the correct class names
.element - the class of the clickable link or image that opens the Thickbox
.overlay - the class of the semi-transparent overlay behind the Thickbox
.close-button - if needed, the class of the close button on the Thickbox