Try with a M49 before the threading code and see if that makes a difference.
Hood

hi Hood

 i tried with M49 before the threading code but it shown up to 1mm pitch shifting.

Ok so if its worse with FRO locked out you have some serious issues somewhere.
Where is the hard bit to determine. As this happens with both PP and SS then it has to be a hardware issue.
You mentioned you had to filter the index so I am wondering if that could be the issue, maybe a better index pulse device would help.
Not going to go back and read to see whether you mentioned it or not but are you using steppers or servos? If servos it could well be your servo tuning is not good. If steppers it could be they are not powerful enough.
Do you have ballscrew or just acme lead screw?
Hood

i am using servo motors for  x &z axes as well as using rolled ballscrew C7 grade.

What type and make of servos and drives?
Hood

I am using panasonic servo drives and servo motor. (2.4 Nm)

You should be able to monitor the following error in the drive software, what errors do you get and what count encoders do you have?
Hood

Because of that things, i tried with schnider motors and drives also but the pitch variation is showing same.

I dont know what to suggest then, only things I can see that could be wrong are  your index is not good, some mechanical parts are moving/slipping or you have poorly tuned servos.
Hood

Hi
Hood, Actually i re tuned motors again but i got same result.

Is there any changes in ss config? so i can change?