shg55:
We stopped using the shields and built the circuit with A4988 driver with a 1.2A 12V NEMA 17 stepper motor.
That is NOT what the datasheet says. The datasheet says the motor current is 2 amps and the coil resistance is 1.04 ohms. Ohm's law will tell you that 2 amps and 1.04 ohms gives 2.08v. If you connect 12v directly to that motor it will try to draw 11.5 amps and the smoke will probably escape.
A A4988 will struggle to supply 2 amps even with a large heat sink and a cooling fan. Either run the motor well below its rated current (i.e. at 1.4 amps instead of 2 amps) by suitably adjusting the current limit on the A4988 or else get a more powerful driver -- perhaps one with a TB6560 chip
We checked to make sure the A4988 wasn't fried by measuring voltage without the motor connected (checked voltage at the 1A, 1B, 2A, 2B) and we made sure the Arduino is working as well.
That does not work and doing that may have fried the driver. The voltage at the motor pins is irrelevant and in any case would only make sense if it was connected to the motor, And then you would need to use an oscilloscope to get sensible data.
...R