Sounds like you may need to rotate your geometry either before or after importing it into MeshCAM. Some CAD programs, like Solidworks, you a coordinate system where Y is up rather than Z.
I've never seen it cut a "negative" image. Can you post the model here? (zip it)
If you tell Meshcam that the tool shank is 44mm, it would have to step over 19mm to step down.
I think the issue may be that the model is too close to the edge of the stock, and MeshCAM won't cut outside of the stock. Try leaving the shank dia. at 6mm, and move the model further inside the stock and see what happens.