Kind of hard to picture this in spite of your attempt at a detailed description.
It would be helpful to see the actual MC file with your toolpath so we can tell you what's wrong.
If you can't post the actual file then I suppose the "modified" version would be better than nothing...
Other than that I wonder if your surface geometry is accurate ?
Are there toolpath filtering tolerances set too loosely and causing this problem ?
Is your stepover small enough ?
Can you extend the surfaces a bit so the toolpath starts away from the actual part a little ?
I could go on and on...