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quicktime and alpha channels

I have posted this issue in may forums and havent't had a response.
In earlier versions of quicktime (5.x) with some applications (flash, etc) you could export your frames or animations as a quicktime file with alpha channels for transparency. For my video work, I need the alpha to be able to have a video running behind the animation. Sin ver 6.x of quicktime, all the codecs that support alpha channels, export the file with the alpha as a white mask, which is useless. I have been told that this is a problem with quicktime, not the applications. So my question is, does anybody know how to do this? or has anoyne been successful doing this? or at least, does anybody know to whom should I direct an email to apple (I have done this in the past and received NO reply from apple) that could help me solve this problem? thanks.

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