This paper examines the use of non-integer switching frequency ratios in digitally controlled DC-DC converters. In particular the execution of multiple control algorithms using a Digital Signal Processor (DSP) for this application is analyzed. The variation in delay from when the Analog to Digital Converter (ADC) samples the output voltage to when the duty cycle is updated is identified as a critical factor to be considered when implementing the digital control system. Fixing the delay to its maximum value is found to produce reasonable performance using a conventional DSP. A modification of the DSP’s interrupt control logic is proposed here that minimizes the delay and thereby yields improved performance compared with that given by a standard interrupt controller. Applying this technique to a multi-rail power supply system provides the designer with the flexibility to choose arbitrary switching frequencies for individual converters, thereby allowing optimization of the efficiency and performance of the individual converters.