> 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.
Render out a Quicktime (animation codec @ best/full, and use a straight alpha channel).
Then, use Adobe Media Encoder to encode the video to the FLV format.
In the options for FLV, choose on2, or Spark compression, but make sure that you enable the compression of the alpha channel.