When adding this little function to your thickbox.js, you can use it to call thickbox from flash.
Things to keep in mind are to make sure, as with most flash files, is to make sure you wmode is set to transparent. I also found that the function on this page does not allow for a caption to be passed. However a simple workaround for this is to pass another parameter through the function and add that variable name to the caption conditional.