Yes, According the trials i conducted for couple of days reducing frequency worsens the problem and increasing improves the things. This is probably becuase The high frequency oscillations [Mechanical] produced when motor is stopped that cause encoder output to oscillate left and right are measured more and more accurately when clock is higher. Higher clock measures most of these oscillations where as when frequency is reduced not all the state transitions of oscillations are measured and there is error stacking every time I stop the motor and start again.

Thanks & Regards,
Prahlad Purohit