>Is there anyway of telling a flash slideshow to stop
I don't know enough able flash to be able to answer that. If you can
interact with it via JavaScript, then just put whatever JS you need to use
as the callback for colorbox.
The JS I was describing earlier would look like this:
$().bind('cbox_open', function(){
$('object, embed').css({'visibility':'hidden'});
}).bind('cbox_closed', function(){
$('object, embed').css({'visibility':'inherit'});
});
It just changes the CSS for flash objects based on the events that ColorBox
triggers.