Hello,
i’ve been having the same trouble, spent a couple of days last week trying to figure out what i was doing wrong… but couldn’t find any help.. i think flash is the problem as the quicktimes it exports seem to be .swf files re-named, hence the small size, so AE doesn’t understand them correctly (there isn’t anything you need to do to the quicktime once in AE, the alpha should show up, if its there). I did try exporting the flash quicktime again from premiere using the Animation millions of colurs+ compression.. but still no alpha.
I gave up with it and am just using .png sequences instead, its slower to export these from flash but at least it works.
Sorry i can’t help.. but then starting to think its not possible, be interested to hear if you figure it out.
steve.