A controller for operating a prime mover of a rod pumping unit includes a processor configured to operate the prime mover over a first stroke and a second stroke. The controller is further configured to compute a first motor torque imbalance value for the first stroke and engage adjustment of a counter-balance. The controller is further configured to estimate a second motor torque imbalance value for the second stroke. The controller is further configured to disengage adjustment of the counter-balance during the second stroke upon the second motor torque imbalance value reaching a first imbalance range.