The collision mesh is generating correctly when using net35 but not when using net46. Some shapes generate correctly whereas others don't. Maybe this is a clipper bug?
I have not yet made thorough testing for which types of polygons generate incorrect meshes. What I could notice by now is that the incorrect generation seems to appear whenever using non rectangular polygons or rectangular polygons with any side smaller than one world unit. I'm using a tile map with tiles of 8x8 pixels and a pixels per unit value of 8 (1 pixel = 0.125 world unit).
I have attached some images for clarification. The first is importing wit net35:

And the next is importing with net46:
