Interesting. I saw that a while back in Bridge from PNG files I received from designers sometimes having that black background displayed in Bridge. I resaved in PS to get rid of it.
I haven't had time to test saving PNG files in PS since the update. I'll keep an eye on it going forward now, though. But is this only as displayed in Bridge and PS recognizes they're transparent? If that's the case, it's a Bridge issue returned, though I never did find out why back when I was seeing this often in Bridge.
Can you find any difference at all between the structure of the files? Alpha Channels, for instance?