Two identical stepper motors behaving differently at higher (but below their rated) speeds
So, we contacted the motor manufacturer. And after analyzing the situation, we came to the following conclusions. I share them here, just in case someone else might one day see similar effects and would like to understand their own motor-problem.


The motors even if they are identical, i.e. from the same supplier and are of the same model type, still have some minor electrical &amp;/or mechanical differences. These are stepper motors, and if we want precise control on speed and position, we probably ought to look into using servomotors instead, was the general conclusion at the end of the dicussion.
The motors were being over-controlled. That is, we had tuned the parameters too tightly for one set of motors and since the motors did have minor electrical &amp;/or mechanical differences, the same set of parameters lead to the other set of motors being "over-controlled" leading to "position control errors".
There was a minor cabling error, which added a further layer of complication to the analysis of the error. This was something new for me, as I had always understood that if the electrical connections for the 2-phase stepper motor are not connected correctly, the motor will not run at all. But as we saw, the motor did run (albeit with strange sounds emanating from it), due to wrong axis connections.


Points 1&amp;3 were the cause of the effects seen during running the motor in an open-loop.

Point 2 was the reason of our original problem.

Hope this info helps someone else in the future in analysing and diagnosing their problem.