Half Res removes alpha on footage

Hi folks

I have a problem, I'm working on a project where I use footage in the Quicktime PNG format with alpha included. But when I turn the resolution down to quicken the workflow, the alpha is dumped and the footage is dispalyed on a black background instead. I full res everything works fine, but that's not an optimal solution.

I've tried to purge all, restart Ae and restart the machine, but still no luck. Any ideas why this is? I've never had this problem before.

Machine:
Xenon E5420 2.50Ghz
8GB DDR800
Caldigit VR 2TB raiddrive eSATA