After Effects :: Using A Keyed Layer As A Track Matte?

I am experiencing a strange issue on a comp I am working with, and due to the way its set up, and the pre-comps etc, I am not even sure how to go about asking the questions!
 
1) To start:
 
I have a comp with 3 Footage layers. One 4K Moving background image from Video blocks, interpreted at 25FPS. One R3D clip of one of our ships, camera on a tripod and ship "Waggling" slightly up and down - kept in RAW mode for clean keying. A duplicate of this layer, used as the colour corrected layer.
 
I have a Comp that contains the RAW footage, Keyed, and the colour corrected footage below it and set to Alpha matte.
 
Above is the settings and the output of the ships wing.
 
This is then precomped, and engine glows, contrails and thrusters etc are added with Null objects, lights, optical flares and particular:
 
at this point, everything looks great, this is then further precomped into a new comp, where it is placed above the background layer - and here is where the issue happens. It is almost as if the trackmatte is a frame or two behind the colour layer:
 
<-- notice the blue edging from the blue screen.
 
I track these layers backwards and forwards through the precomps, and I cant figure out why this happens?
 
(there are keyframes on the trackers above, and the contrail precomps for position, and a scale change over time on the ship layer in the final comp.) If I pull the ships precomp into the final comp as a new layer - the issue remains. If I double click to open the ship layer, the issue is not visible.