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Well, what's the settings in the Avid? By default it will invert the Alpha, you may need to invert it in the Alpha key's settings by ways of the effect editor. Also make sure to choose the Alpha in the first place. If it's not been selected on import in the options, it will never appear once the system has converted the clip.
Check the QT in AE or Photoshop CS4. You should see a transparent BG.
You should also see alpha info in the .mov properties and in the description field in AE.
Hooray! When I imported the Quicktime into AE and played it, the transparency was there! Thank you so much! You just saved me from hours of frustration. BC