First off, appologies for posting this in the general section as well as here.I posted by mistake in the general section.

I have a scene of a space craft that passes the camera, heads towards you and banks away, the camera turns to follow it. This is rendered out to a RGB channel and an Alpha channel. The rgb plays fine no problems, as does the Alpha channel.
Now, I use the same camera that I used in the RGB shot, to render out just a star scene. This camera tracks exactly as it did for the RGB space craft render.

Now the problem starts. As soon as I composite these images together in Lightwave, the resulting video gets a periodic slight stutter, especialy where the camera turns and follows the spacecraft as it banks away, against the stars.
I've tried compositing it out on another computer with a different graphics card. I've tried multiple codecs, but nothing gets rid of this annoying hiccup in the finished video.

Just to recap. The RGB stream as a video, plays fine, no hiccups. The problem seems to be when they are composited infront of the star background, which is animated by the way, so the stars are also moving.

Any ideas?