It appears that (1) value orders are not consistent in Parallel Plot and Graph Builder and (2) when not selecting all variables in Points overlay, selected ones insist on showing up at left instead of with the correct columns in the Parallel plot.
Maybe there is a reason that different variables can be selected for Points element vs. for Parallel element, but I can't imagine what that would be.
Here is some code in case you are interested in replicating this issue.
dt = Open( "$SAMPLE_DATA/SAT.jmp" );
dt << Graph Builder(
Size( 854, 668 ),
Variables(
X( :"2004 Verbal"n ),
X( :"2004 Math"n, Position( 1 ) ),
X( :"2003 Verbal"n, Position( 1 ) ),
Color( :State )
),
Elements(
Parallel( X( 1 ), X( 2 ), X( 3 ), Legend( 3 ) ),
Points( X( 3 ), Legend( 4 ) )
),
SendToReport(
Dispatch( {"Points"}, "", OutlineBox, {Close( 0 )} ),
Dispatch(
{},
"Graph Builder",
FrameBox,
{DispatchSeg( ParallelAxisSeg( 1 ), {Transparency( 0.25 )} )}
)
)
);