If I am reading your toolpath setup screens correctly, you are using two different bits one for pocketing the wood, another for machining the aluminum…that can easily account for your problem; between different flute geometries and the fact that bit sizes are nominal (not perfect), you don’t get a fit unless you use the same bit for both toolpaths. You might try using your calipers to get exact diameters on each bit and adjust accordingly in your tool database, or find a bit that is usable for both wood and aluminum and use it.