For those of you wondering why most flash applications leave wmode as window, it's simple because wmode opaque and transparent breaks a bunch of flash behaviors.

It creates performance problems, it creates browser incompatibilities, and in general makes flash worse than usual. (It also breaks accessibility, but I'm not sure if people care about that for ads)

Mode details: http://justin.everett-church.com/index.php/2006/02/23/wmode-...

This page has a good list of known wmode related bugs: http://xebee.xebia.in/2010/08/29/the-wmode-nightmare-in-flex...