Embodiments of the present invention relate to machines that perform in-system programming of programmable devices that are attached to assembled printed circuit boards. In accordance with one aspect, multiple nonvolatile devices may be programmed in a single session at their normal maximum programming speeds. Different nonvolatile devices on a board can receive different data. Data variables can be inserted so that not all boards receive identical data. A master controller sends image files and algorithm information to a subsidiary controller. The subsidiary controller executes a device algorithm, and an FPGA executes a bus algorithm. Embodiments of the present invention can be designed as stand-alone systems or to operate cooperatively with an automatic tester, so that testing and device programming can take place in a single operation using a single fixture to hold the circuit board.