I am using your product https://www.pololu.com/product/2980/specs the A4988 Driver at 1/16th microstep rating
The Three Steppers I am using are rated for 2x 1.5 A, and 1x 2A stepper
The 2x 1.5 A have geared heads on them
I am experiencing some accuracy issues with the steppers, they are driving a very very light load. Because I am using the a Continuous Current Per Phase that is less than my motor current could this cause lost steps?
There are probably several factors that are contributing to why your motor is missing steps, and running your motor below its rated current is definitely an important one since it means your motor has less power to handle the load. We have several stepper motor drivers that can handle higher currents than the A4988, so you might consider one of those:
Running your motor at more precise microstepping resolutions, high step rates, and low voltages can also increase the likelihood of it missing steps, so you might consider adjusting those parameters as well. I would also recommend verifying that your power supply is appropriately powerful enough for your motors.
Microstepping does not increase the accuracy of a stepper motor. In fact, microstepping often decreases accuracy.