> I have managed to remove the black background in After Effects using a plugin called UnMult, but when I try to render as a FLV file in AE, even though I check the option to preserve the alpha channel and encode using the On2 VP6 codec, I still get a black background.<
Are you absolutely sure you don't have the alpha? It's possible your viewer is just showing black because that's what it defaults to with transparency.
That issue with alpha viewing is often quite simply solved but I am NOT familiar with Flash's various codec functions. There are only a few codecs that will support alpha. In many codecs, the checkbox for preserving alpha actually accomplishes nothing since the codec cannot support the information. Also, you must choose "millions of color +" regardless of the preserver alph setting.