If you were running AB and called them and talked to Doc, I'm fairly certain the first thing he would tell you to check is your scope tracking. A tracking error is the simplest explanation of your results, and they see it all the time. NO brand is immune (although some are common offenders while others are rare, but still occur occasionally). Bottom line - unless you've REALLY checked it, don't assume it is correct. Check it. That is the simplest explanation.
That said, I own a MS3 and a Labradar. I have run them simultaneously and they never disagree more than 4 fps, usually less. Both are extremely reliable, and are far superior to the optical chronos. Nowadays I only run the Labradar, because the MS3 does result in POI shifts (lower impacts). That "could" also explain your problem, but reading your post carefully it seems that you aren't just experiencing this with the MS3 attached. Like many here, I have experienced cases where the Labradar and the Kestrel AB using one of their custom curves matched perfectly all the way out to nearly a mile. No MV calibration or Drop Scale Factor corrections were even necessary. Then, changing lot numbers of of the same factory-loaded ammo not only changed the measured MV (negatively), but also the MV and DSF calibration became necessary because the bullet was still under-performing the calculations based off the new, lower input for the accurately-measured MV. I've not seen anything like a 75 fps correction needed, though. More like 10-20. Something is definitely amiss with a 75 fps correction being required, and it doesn't sound like a chrono issue.