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A port of a class in a composite structure diagram is not always shown. Depending on how the user makes the port visible, the initial layout is different. It's possible to show ports via (1) the Show/Hide dialog (F4) (2) by activating model/diagram synchronisation (3) by explicitly dragging it to the class border In case of (1), the ports are vertically layout, starting from the upper left corner, in case of (2), the ports are horizontally layout on the upper edge (around the middle). In case of (3), the user provides the explicit position of each port. There is no good reason, why (1) and (2) result in a different layout. The bug is also related to a useful initial layout for ports on parts, see bug 527181.
Created attachment 271846 [details] Figure showing layout problems