Probably something you've already aware of but what format are you rendering out to?
If the output format doesn't support a matte channel (e.g. dpx, cineon, most quicktime formats, etc) you will see correct images in viewers but the output will not have a matte. So depending on how you look at the output (by reading it into Fusion itself, for example) you will see a black (blank) matte channel. This is true of any comp, not just ones using Primatte.