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The problem occurs after showing compartment that are not visible by default. The figure seems to be correct, but the underlying "layout" is probably incorrect, in other words the diagram works as if the compartment where not at the same position as their graphical representation. The result is a lot of creation issue and exception after visible compartment modifications (note that default visible compartment modifications in preferences are not affected). All diagram are affected by this issue (also see bug#319223)
Fixed in r5141. (https://bugs.eclipse.org/bugs/show_bug.cgi?id=319223)