Alan:
Originally I rode hundreds of miles while operating a Jones simultaneously with a Protege and results were always exactly the same from both meters. I have never seen the occasional loss of a count with the Protege.
Probably it is not very wise to blame poor results on the Protege when your course is so bad that your ability to duplicate your path is in doubt. You should make tests on a regular street where final rim readings should be within 0.1 rev for a course of about a mile (which of course does not have to be calibrated).
One way to test that a Protege is operating correctly is to use it with another simultaneously. Of course you can use a Jones simultaneously.(Why are you not doing this already?)