So as the title suggest my toolpaths between the flat areas and the filets are not lining up. If you run simulation and then zoom in to where the upper plateau meets the lower plateau you can see the flats machine over into the edge of the fillet. You may have to click the refine button to see it. I've checked and double checked my settings and haven't found a reason for this as of yet. The results on the finished part are the same. I had the same results on another smaller but similar part. I double checked the physical tool lengths also. I'm attaching the file hoping someone can figure out if this is me or a bug.

Thanks, Forrest