The stepper motor runs "open loop" so the controller has no way of knowing the position of angle of the tracker. It keeps track of the step count each time the motor is stepped so, as long as it starts up in a known position, and isn't allowed to stall at all, it all works fine. 

The controller also has a 'clock' which counts the milliseconds that have elapsed since powering on. After each step, the controller calculates the exact clock time of the next step. It does this using a bit of maths which relates the step count - and therefore the position of the nut - to the angle of the moving part of the tracker. The angle must increase at a constant rate, but the timing of the steps is changing slightly all the time.

Once the calculated clock time passes, the motor is stepped again and the cycle repeats.