Just in case there are some more Flex developers out there who haven’t spent the last 5+ yrs coding Flash apps ;)… To get a fill transparency of your Flex app sitting in an HTML page, backgroundAlpha is not enough.
You also need to set the wmode attribute of the object/embed tag you’re using to place the swf on your page. Don’t forget to do that also in any JS code you might use to embed the SWF in your page (that was what I was running into for the last hours – args!).
Here’s a link to a flexcoders posting describing the whole topic again.