Hi Joe,
The medial-axis carve will only cut as deep as the flute length of a V-bit, and only as deep as the corner radius of a ballnose cutter.
Make sure your canvas Z size is deep enough to accommodate the depth of the cuts that are needed - along with the layer's Z size, unless you modify your contour Z to stay within the layer.
For example:
The V-bit is a 90deg 1/2" diameter and has a flute length of 0.25", so that's as deep as it will go. The canvas + layer Z size is 0.25" to accommodate the full flute length of the V-bit.
Hope that helps!
- Charlie