Boiler systems and associated control systems, methods for operating same, are described herein. In one example embodiment, a boiler system includes a furnace, an exhaust passage, an air passage, a FGR passage, a flue gas valve that is adjustable by way of a first actuator, a NOX gas sensor, an oxygen gas sensor, and an additional valve that is adjustable by way of a second actuator. Further, the boiler system includes at least one processing device coupled to the NOX gas sensor, the oxygen gas sensor, the first actuator and the second actuator. The at least one processing device is configured to generate control signals that are provided to the first actuator and second actuator, and also configured to generate correction factors by way of a calibration process and to utilize one or more of the correction factors in determining one or more of the control signals.