You are loosing steps in the Encoder or Step input. Most likely the encoder
Zero the drive (turn off power then on) and Zero mach. Make a mark on the motor shaft.
Run your program, then tell the machine to go back to zero.
Read the drive's M command and it will show Encode and Step input counters.
( The M and S are going to be close since the drive is trying to make the zero)
If the S setting isn't zero then you are loosing step input pulses between the BOB and drive.
If the S is zero and the motor shaft is off, then you are loosing encoder counts.
Is it a single ended or differential encoder ? Are you using twisted pair cable
?
Larry K
Manufacturer of CNC routers and Viper Servo Drives
www.LarkenCNC.com and www.Viperservo.com