Heya Rune, you have quite an unusual issue here. If coverting the QT PNGs to the Animation CODEC results in the same issues then it is likely an AE issue rather than the source footage.
I can only suggest deleting prefs for a quick fingers-crossed solution that it isn't anything more serious.
But before doing that I would render out short section, with settings that allow for an Alpha - to check if it's just a preview thingy as opposed to having the issue reflect itself onto a rendered movie.
Oh DAMN! Having typed this much, I do recall having an issue with alpha-laden QT PNGs. It was a request from the Disney folks here. I ended up going either uncompressed or Animation. So, try converting/rendering the PNGs to Uncompressed.
Good Luck
RoRK
broadcastGEMs - AEPro Volume 02 (Professional Adobe After Effects Project Files - Now Available).
Adobe After Effects Training in South East Asia.
