The short reason is that MeshCAM only has .01" of accessible area to drop the cutter in the slot and machine it. If the surface geometry is very smooth around the slot then MeshCAM may skip right over it and not even check if it's there. I have three things you can do to improve the situation:
1) Make sure you're using V4, not V3. V4 looks at the surface much more closely to find this kind of thing.
2) Reduce your tolerance value. The tolerance defines how closely MeshCAM evaluates the geometry to look for sharp details.
3) You can always use the V4 "Define Region" command to only machine the areas with the slots and use a much finer tolerance only on that part of the model.
Let me know if this helps,