Flash objects and z-index

Recently I was working on a rich-media project and I got some issues.
I had problem when I was trying to combine DHTML, layers, LightBox library and FLASH object on a single page.
The problem is that the FLASH object always stays on the top of all layers, regardless the stacking (z-index). This problem is also described in Adobe (former Mactomedia) tech-note.
The only solution (described in the same tech-note) is to use the "WMODE" parameter for the flash EMBED / OBJECT and make the FLASH movie transparent. Well, if the flash movie is not designed to be transparent, it will not be. But now, when we have successfully set the wmode = "transparent" the stacking of the layers works just fine.
OK, good. Now it comes another issue: what happens if the FLASH object is automatically generated Banner that comes from a banner rotating system ? Luckily I am using the phpAdsNew, and they provide option at the banner properties to make the Flash banner transparent.
Thanks goes for http://manisheriar.com/