Problem with aLpha channel export to quicktime

Hi! after hours of trying this here is my last hope:
I masked an imported qt-movie with chroma key a person in FCE 4. That was fine. But when I export Quicktime (million+, without compressor, etc.) there is no alphachannel anymore. I need that for the web (FLV). I f I export FLV FCE freezes at 0%.
I am shure out there is somebody who has an idea. Pleaes

Do not render the contents of the sequence. If you render, the sequence is exported using the render files. With the sequence unrendered export using the Animation codec with colors set to millions+.

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