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This has been confirmed as a bug in OG's automatic layout code.

Ver 0.81 and onwards of the Tree Tool script can now correct this – restoring all row gaps to the exact rank separation value specified in OG's automatic layout inspector.

To use the script to simply fix the row gaps in Automatic Layout's own output, without converting the tree to an orthogonal layout (parents centered over children), use the c=false switch.

(Tree Tool can also be used to rapidly change shape size, row and object gaps, magnets, link type, fill, stroke, shadow etc.)