I have a Flex application with wmode=transparent and a transparent section that allows whatever is underneath it on the HTML page to show through. In this case, what's showing through is another Flash application. This works fine, but I can't interact with the Flash application showing through.
I tried setting the z-index of the Flash app to something greater than my Flex app, and that worked, but unfortunately that solution doesn't work for my case because the Flex application has components that occasionally overlay in that area, and setting the z-index of the Flash app to be higher means those components are always stuck behind it. Also unfortunately I don't control the loading of that Flash app, so I can't load/embed it into my app to get around this problem.