Re: Boundaries
It looks like you are using a "stock aware" operation (Advanced/Adaptive Rough, Z level rough, etc.)
In short, BobCAD looks at the geometry you want to machine, sees all that stock (in shaded blue) and tries to remove the excess. Your boundary is including all that space to right where there is "stock" but no geometry. It's trying to remove it.
Shorten up your boundary to only include the areas where you have selected geometry. The boundary needn't be 2D but it must be a closed shape. You can get creative.
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Mastercam X9/2017 Multiaxis for SolidWorks - Bobcad V29 3ax Pro 4ax Std.