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With the proliferation of multi-gantry automated stacking cranes, the already difficult crane scheduling problem in container terminals has become even more challenging. In this paper we present an efficient algorithm that can solve a sub-problem that arises in this context, namely the prioritization of crane gantry movements once transportation tasks have been assigned. We tackle this problem for both, twin crane setting and crossover crane setting, and develop graphical models and strongly polynomial algorithms accordingly. A series of experiments is carried out where it is shown that the method can produce optimum solutions with exceptionally small run times.