If you have low count encoders, the position will be in steps no matter the CV mode or not. It may be this or that your geckos are not properly tuned and you have a constant overshoot-correct, overshoot-correct action in your closed loop which gives you a jagged oscillation.
Also could be your file generation. If circles are coded as circles but arcs are coded as linear interpolated segments, it could seem jumpy. Try increasing the accuracy of the linear interpolation to smooth out the transitions.