A refrigerator appliance configuration, and associated methods of operation, for an appliance with a controller, a condenser, at least one evaporator, a compressor, and two refrigeration compartments. The configuration may be equipped with a variable-speed or variable-capacity compressor, variable speed evaporator or compartment fans, a damper, and/or a dual-temperature evaporator with a valve system to control flow of refrigerant through one or more pressure reduction devices. The controller, by operation of the compressor, fans, damper and/or valve system, depending on the appliance configuration, synchronizes alternating cycles of cooling each compartment to a temperature approximately equal to the compartment set point temperature.