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I think I can answer number (2) now myself ... it only occurs if I ask for the StructureDescription of the automorphism group, and then I ask it to output the graph (eg by typing gap> graphname;), but NOT using the "Print()" command. So in invoking the StructureDescription I seem to be switching the field of "autGroup" inside the GRAPE structure of a graph, to equal its StructureDescription instead; however only in one particular slicing of the data. BY THE WAY this DOES occur for normal command-line gap_console() inside SAGE - ie you do not need the notebook as I previously thought.