My (limited) understanding is that the Flash plug-in for browsers works outside of the browser's page rendering engine, so settings like z-index don't affect it. It's like PC games that write directly to the screen, rather than through the operating system API or drivers. In other words, there's no fix or workaround.
Ouch - that's not what I wanted to hear. I know that I can modify the popup js to remove the flash item before it is activated but putting the flash back when the popup is closed is going to be more tricky. I'm sure it can be done though, I just hoped a simpler solution may be available.
Ok, I can see why this would not always work because of the transparency showing the background through parts of the flash content but for Flickr slideshows and YouTube vids underneath the popup, this seems to do the trick, they're not interfering with the popup opaque layer now. Thanks to you both.