I am scanning a hexalobe and it is scanning good. The problem is in the report. It doesn't show where the scan is scanning and reporting the part way out. Why don't they match up closer? Here are some pics.
Tried an alternate method? Put a micrometer on the lobes and see if it's undersize. Put two gage pins onto the inside radius and mic it. Oversize? Numbers close to what the CMM shows?
I've had some questionable CMM results that turns out to be a really jacked up part because a tool broke.
Try slowing your scanspeed down. Looking at the profile analysis, it might be that the machine is moving too fast in the larger arcs (almost a straight line).