No experience here, but definitely an interest in printing and building a 3DOF hexapod or quadruped. Trouble finding simple beginners tutorials and firmware for inverse kinematics and movement. Well, that and I am still trying to get my 3D printer working so I can build the frame.
However, I am wondering if your issue is power related and your servos / drives are experiencing brownouts. Double check your power requirements and make sure your power supply is strong enough.
I am not familiar with harmonic drives. If you were using simple hobby servos though, I would imagine the PWM signal is getting cut off. Without a constant signal to set the angle, the servo resets to the default. Perhaps your microcontroller can only maintain so many PWM signals at once.