Can you email me your last few measurement files of your 21 step target and your unlinearized .quad file that you used to print it (you could send your .qdif/.text file too). I will take a look in to see what is going on there. I have been messing with an idea for fixing these kinds of problems and this would be a great test. No guarantee that I can fix it, but I'll give it a shot.
Richard Boutwell
Email these to Richard@RichardBoutwell.com