Unplugging the batteries and leaving the robot for some time can cause other issues. The encoders can get to a state that makes them lock up and you need to reset them manually by putting a jumper on the encoder (the jumper depends on what motor you need to reset). Also this will cause you to loose all you home calibration so you will have to reteach.
From what you are describing, you could have a problem with a servo pack, the harness in the robot or a motor.
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