Those settings determine whether a motor is energized while idle. Its common to shut down Z motor while not moving Z to save power, since a screw driven Z cannot be reverse driven by the weight of the axis. Your firmware is set to energize all motors at all times, which uses a little more power but is better for print quality.
Microstepping is not under firmware control, the jumpers simply supply voltage to the microstep pins, or not. For 1/16th microstepping, all three MS pins on the pololu should read 5V. Meter all three pins, if any of them are low then you know where to start looking for a bad solder joint.
Microstepping is not under firmware control, the jumpers simply supply voltage to the microstep pins, or not. For 1/16th microstepping, all three MS pins on the pololu should read 5V. Meter all three pins, if any of them are low then you know where to start looking for a bad solder joint.