First of all, very nice model!
I don't think m2s creates a mask from a movie with an alpha channel(it might do a mask but not a good one), if you separate the alpha that is a different case.
What I used to do was to render the alpha in a movie itself, or if you have transparent areas make materials that are 100% white and luminous and render those in a new movie. On the mask It's nearly always better to interpret the grey areas (usually from antialiasing) as part of your object, since this will include a black line around your ship, this sometimes look weird over planets, but most of the time it keeps the antialiasing of the color image, and looks much better then the sharp transition you would otherwise get. This really does not matter unless you really want the best looking ships.
You should also render with an isometric camera or something close to isometric. A perspective rendering might look very weird depending on how large the perspective is.
Anyway, I hope this was not old news, I just remembered all the frustration I went through to get my ships looking like the originals.
This post has been edited by Modesty Blaise : 05 May 2010 - 05:26 AM