IE6 has known issues with transparent images (IE6 has A LOT of issues). There are numerous javascript fixes for this - but they all work basically the same way with a 1x1 pixel GIF. If you have the ability to go with JPGs or GIFs instead, that would save you a lot of heartache - but I would guess you would have already gone that way if you could have.
One way I've dealt with it in the past is to detect the browser and swap in a non-transparent image (GIF/JPG) if it is IE6. This is approach has many challenges as well and will end up being a significant effort.
The bottom line is that IE6 is just a pain in the rear. You might want to try one of the other IE6 transparent image solutions to try to avoid the conflict, but I wouldn't be optimistic on coming up with a clean execution.