SUCCESS!
So I just completed a test piece that used both the 3D 2 rail cut, a VCarve, and a pocket.
All cuts did exactly what they were supposed to do.
I theorize that the loose collar only showed up when I did the 3D cut and not the othercuts was because the rotation of the indexer was around one degree per step for the 3D, and the shock of the motor trying to turn the gearhead caused minute slippage with each step of the motor.
That is why rotating manually to verify that the 360 degree rotation was accurate did not reveal the problem, as the slippage was not so severe that the slower and less jerking rotation allowed the motor to turn the gearbox without slipping.
Regardless, it looks like it is now fixed, and I can keep what little hair I have left to pull out another time.
I will create some more parts soon, and hopefully no further issues will surface.
I want to thank everyone who took the time to respond with suggestions.
Bob