Abstract: The present invention allows large glass substrates to be rapidly moved from one processing station to another. Such movement occurs such that drives in different chambers are synchronized to move the glass substrates on shuttles at appropriate times. In systems according to the invention, at least a first and second chamber are provided. Typically, the first chamber is a load lock and the second chamber is a processing chamber. A substrate transfer shuttle is used to move substrate along a guide path defined by, e.g., guide rollers. Drive mechanisms are employed for most chambers to drive the shuttle along associated portions of the path. A control system is provided which powers the drive mechanism for the first chamber to drive the substrate transfer shuttle from a first position toward a second position and through an intermediate position. At the intermediate position, the substrate transfer shuttle begins to engage and induce movement of the drive mechanism for the second chamber.