I can't find an official change log for this upgrade, but what I found on mine is:
1) Mark all as read when closing Popup
2) fixed the muted applications.
Both are great updates, I like the ability to mark emails/sms as read just by closing Popup instead of having to go in and look at them.
It really frustrated me that I couldn't add Slacker radio to the Muted Applications before. Now when I'm at the pool and listening to Slacker, I don't get a bunch of email popups.
There might be other enhancements, but I haven't found them yet.