Repeatability Error

Please see the attached time line. this is the what actually happening.
for one side it go excess distance than jogging distance. for other side it going correctly as per the jogging distance. hope you will clear now.

How big is the error for each movement?, and how big is the movement?

This could be a electrical noise issue in the step/dir lines or perhaps a timing or step polarity issue

As well as PCW's suggestions, if it is just a parallel port interface, it is possible you may only be getting a 3.3v signal from the port. this may be a marginal signal for the drive. What brand/model of drives are you using? Do you have a breakout board?

May I repeat a previous question. Do the joint position command numbers act as expected?

If the numbers are the same but the positions are different then the problem is in the hardware
If the position command numbers are different then the problem is in LinuxCNC. (probably in the kinematics)