A glitch duration threshold is determined based on an allowable dose uniformity, a number of passes of a workpiece through an ion beam, a translation velocity, and a beam size. A beam dropout checking routine repeatedly measures beam current during implantation. A beam dropout counter is reset each time beam current is sufficient. On a first observation of beam dropout, a counter is incremented and a position of the workpiece is recorded. On each succeeding measurement, the counter is incremented if beam dropout continues, or reset if beam is sufficient. Thus, the counter indicates a length of each dropout in a unit associated with the measurement interval. The implant routine stops only when the counter exceeds the glitch duration threshold and a repair routine is performed, comprising recalculating the glitch duration threshold based on one fewer translations of the workpiece through the beam, and performing the implant routine starting at the stored position.