Yes.
Place the html object for the flash before any part of your display of your script images.
Let me make that clearer.
Any html elements that display images as the result of your script must follow the flash html object in your page's source code.
Also, you can use the style attribute on any element to indicate it's z-index. This tells the browser how to vertically "stack" the elements.
Make the flash object's z-index 0 (zero), and any other elements you wish to appear ontop of the flash, set their z-index higher than zero. You may have more complications that I'm not aware of yet. So, if you don't find this solution to work satisfactorily for you, drop me a note. I'll be happy to assist.
zetacon4@comcast.net