Make2d Tuning Suggestions?

I am having a lot of problems with Make2d that persist with V6. The general cause appears to be bleed through. Attached is am example. I have a grid line that goes into an undercut. The hidden grid line roughly follow the path of the black line. Then the hidden grid lines start to bleed through.

There are some other examples of bleed through. The incomplete oval. The line opposite (crossed from the circle) is another oval that has bled through. The circle inside the rectangle bled through.

I see that tolerance affect the output. Is there any tuning that can be done to get rid of bleed through?