Looking at your toolpath files and I would say that the Allowance for the Roughing toolpath is forcing the cutter to initially run above the material surface. If you leave the toolpath running it should cut into the material. You could almost certainly run this 3D project without a roughing toolpath.
If you run the Finishing toolpath this should raster across the the material slowly dropping into the material.
Cut3D offers more efficient / better roughing strategies than the Free Vector Art 3D Machinist software.
When having these types of problem I would suggest emailing your questions and associated files to - email@example.com - and we can usually get straight back to you with ideas and suggestions.