Have you played with (before you bring the PNG into your timeline) with right clicking on the file, going into properties, and specifying that it has alpha, and trying ether Straight (Unmatted) or Premultiplied? Then dragging it into the timeline?
This is what I have to do for video files with an alpha channel.
Be curious to hear if you get this to work, as I might be doing some work with a batch of PNGs in the near future.
I'm mystified - I use .png pics all the time and have never had any problems in either v8 or v9, I just drop them onto the timeline. I suspect some Preferences setting has somehow been set oddly? (Possibly even for just this particular project - it could be worth testing this by starting a new project and dropping a few .pngs into its timeline just to see how they look.
Does the transparency work correctly on the preview screen?