The new code:
if (window.top != window && browser.firefox() && version < 9) {
div = "needsFlash9Upgrade";
means you need majorVersion 9 or higher. But it looks like the real kicker is the window.top != window which (someone who knows for sure) means the iframe is what is "breaking" the Jar (and why the workaround works).
In other words, if you're using PJ (which sticks the player in an iframe) and Flash version is less than 9, you'll get the needsFlash9Upgrade div displayed instead of the pandora player.