Agree with Turbo. I have had KEB and GAL on site at the same time about this machine. When you use the Synthetic pre torque on the KEB drive setting( synthetic pre torque means you are not using any load weighing device),you are allowing the drive to estimate the amount of torque needed to hold the motor still while the last brake lifts but it needs a run first to calculate this value. This means when it reverses direction KEB resets the pretorque setting to 0 so it can measure that direction which gives you this nasty bump and creaking noise from the brake when it lifts. All rides in the same direction after that first run are good.
These machines MUST have load weighing installed, calibrated, and adjusted while using the normal pretorque setting on the drive to properly pre torque the motor without KEB guessing due to the machine brake design.
There could be an encoder issue only if the tolerances of the encoder are rated high. Garbage encoders give garbage feedback.

Hope this helps.