Made a little video of some flames in front of a green screen, it is a SWF file. Imported it into After Effects. Used the KeyLight effect to add an alpha mask. It looks good on the AF viewer, but doesn't render without a background. Used both AVI and MOV codecs, checked the RGB+Alpha, Set to Million Colors+ and it renders with the background instead of Alpha. Also toggled the little checkered square at the bottom of the composition screen. It all looks good on AF, but does not render without the background, no alpha.
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