I am having a Flash issue as well. But I might be able to help you with yours. I have a Flash navigation bar in my header using STS. Mine shows up just fine. I used absolute addressing for the swf instead of relative. Check to see how you are calling for the Flash file. If it is a relative address, try starting with http:// and go from there.
The problem I am having is a real mystery to me. My Flash navigation is for pointing to 5 of the main categories. I have used the absolute category address for the buttons within the Flash movie. Outside the store pages everything works. It goes right to the category page from anywhere. I have used it in the main directory, a page inside a sub-directory, and page inside the "catalog" directory that I created for test, and on both html and php pages. But on store pages the swf shows up fine, the mouseover effects work (including and image change and a sound effect) but the hyperlink takes you nowhere. When you click nothing at all happens.
Does anyone know of any conflicts between Flash, oscommerce, and or STS? I'm using on (release) {getURL( .... on the buttons within Flash.
Thanks.