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We study a disturbance rejection problem in a production pulsed light source, used in semiconductor photolithography, to yield quantifiable and guaranteed improved performance over existing control techniques. The disturbances of interest include an offset with reset properties and sinusoids which appear aliased in the measured data which is available only at pulse events. The light source is pulsed at varying rates yet actuators move in continuous-time, yielding a system which blends aspects of continuous-time and variable-data-rate discrete-time. We employ novel modifications to standard continuous-discrete Kalman filtering ideas for disturbance state estimation and establish and solve a non-standard regularized minimum variance control problem within a disturbance rejection framework. The controller as discussed is now in production in semiconductor lithography manufacturing lines. We analyze data from these production light sources and show the controller has the capacity to remove aliased sinusoids from the measured output and yields operational performance levels provably close to optimal for the hardware.