Encoding with an Alpha Channel Using Quicktime Pro

I am pulling my hair out trying to encode a green screen video that will play on a website so the website shows through the transparent alpha channel. Problem is when I encode to .flv or .mp4 the alpha channel is never retained even when I check "encode alpha channel" in the .flv export setting window. I have downloaded a trial version of Sorenson Squeeze and even that couldn't retain the alpha channel.
The video I am using was exported out of Final Cut Pro 7 using Quicktime Conversion using the Animation Million of Colors PLUS codec and when I test that it does indeed have a transparent alpha channel so something is happening when Quicktime Pro is encoding it.
Can anyone recommend a way to export a .mp4 or .flv with the alpha channel?
Thanks in advance for any help you may be able to give.
Benjamin Jones

You can also export a RGB video (without alfa) with any codec, and a second pass with obly alpha - it depends if you need that as a final export (then use codec than can export alfa) or intermediate format (then you can use image sequence or 2 pass video).

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