It sounds like you’re describing two different issues –
1) matchframe error
2) getting the alpha to work as expected
For (2) I suggest that you create a composition for the RGB and Alpha layers. Place the RGB layer below and set it to use the above, Alpha, layer as an Alpha Track Matte. Then nest this composition into your ‘final’ comp.
For (1), I am assuming that you have made this sequence a 3D layer in AE. Not knowing more, I am assuming that this sequence should be left as a 2D layer. If this doesn’t work, then you will have to let us know more on the following –
(a) the tracking or background plate/layer; provide at least an image (b) how was the HVAC created in relation to the tracking plate
(c) what you have done to both these layers once you brought them into AE.
Cheers
RoRK
Intensive mocha & AE Training in Singapore and Other Dangerous Locations
Imagineer Systems (mocha) Certified Instructor
& Adobe After Effects CS6 ACE/ACI