For page, group, and wrap variables you can set a column property defining the value order and then use that to be sure of which plot is which. I often want to change the column or level names anyway and now this can all be done in a transform column:
Open("$SAMPLE_DATA/Big Class.jmp");
pageOrder = {"Female", "Male"};
Eval( Eval Expr(
gb = Graph Builder(
Size( 378, 714 ),
Show Control Panel( 0 ),
Show Legend( 0 ),
Variables(
X( :height ),
Y( :weight ),
Page( Transform Column( "Respondent Sex", Nominal, Set Property("Value Order", {Custom Order( Expr( pageOrder ))}), Formula( if(:sex=="M", "Male", "Female" ) ) ) )
),
Elements( Points( X, Y, Legend( 8 ) ), Smoother( X, Y, Legend( 9 ) ) )
)
) );
Side note: The GraphBuilderGroupBox you referenced probably does not contain that text, note that if you set the visibility to hidden the heading is still there. I think this element just doesn't show up in the tree, sort of like how individual points aren't in there. It would be nice if both were accessible!