Are you rendering using an Avid codec? If so, here’s something that may be causing your problem…
First, make sure your comp is 720×486 D1 NTSC, because Avid Uncompressed or Compressed codec requires it. And make sure in the render queue you have rgb+alpha selected with the proper alpha settings (premultiplied for hard edges, straight for soft edges and gradiation)
Second, if you’re using any Avid codec to render out your quicktime from AE, then make sure when you import into Avid you select “use existing” for your alpha channel option. Many people instinctively select “invert existing” out of habit, but the Avid codec in the quicktime already inverts it as it should be.
You can also invert the alpha after importing it into Avid if you need to. You place the clip into your timeline, open up your effects editor, and invert the alpha from there.
If this doesn’t help, give some more details about what your trying to do.