Make graph builder's Color obey Value Color column property even when same color is chosen for multiple values. When using overlay the colors are as they are set in column properties.
Names Default To Here(1);
dt = Open("$SAMPLE_DATA/Probe.jmp");
dt << Clear Row States;
Column(dt, "Site") << Set Property("Value Colors", {1 = 16, 2 = 16, 3 = 16, 4 = 16, 5 = 22});
gb_color = dt << Graph Builder(
Size(530, 459),
Show Control Panel(0),
Variables(X(:Start Time), Y(:DELW_PCOLL), Color(:Site)),
Elements(Points(X, Y, Legend(3)))
);
gb_overlay = dt << Graph Builder(
Size(530, 459),
Show Control Panel(0),
Variables(X(:Start Time), Y(:DELW_PCOLL), Overlay(:Site)),
Elements(Points(X, Y, Legend(3)))
);

Currently I use a workaround where I create new column in which I group the columns and set value colors to that column. It does work but it is unnecessary extra step and prevents be from interactively selecting different values based on the legend.
@jthi Thank you for submitting your wish! We hope to include this in the next major release of JMP! Be on the lookout.
Hi @jthi, thank you for your suggestion! We have captured your request and will take it under consideration.