You know you are losing steps because the travel is not as programmed, ie DRO will read the correct distance but the axis hasnt moved that distance. If you have steppers then you may also hear it missing steps, it will whine.
Gaining doesnt sounds like you dont have your steps per unit set up correctly, however if you are saying it only happens sometimes then that cant be the case. What kind of setup do you have, what drives, motors etc and what type of machine. The more info about your hardware the better.
Some drives require pulse lengths to be longer than others, 5 is the highest you can set here but if you need longer then try the Sherline mode.
Hood