I have seen this problem many times. The error is in the tolerance. For finish 3d machining a tolerance of .0003 seems to work best and make sure you use the arc filter that is in the tolerance tab. Iv'e never used the one way filtering option but I set the filter ratio to 1:1. If you are doing roughing or semi finishing you do not need to run such tight tolerances. If you leave .020 stock remaining a tolerance of .005 is fine. At .010 stock remaining I use .001. You can actually see the facets in the verifier when you use different tolerances. You need to zoom in to see them but they are there. Hope I could help