Flash & DHTML - Why is SWF always on top? Can I do anything to change it?

I have a website that has a live help section. It incorporates a “fly-thru” help button that users can click on to activate the live help. The page also has SWF files. The problem is that when the “fly-thru” button well, flies thru, it goes underneath the SWFs. Does anyone have any idea how to fix this?