It seems that internally when the Minimum Size Split in preferences is unchecked ( <<Off ) the default that appears in the options is 5. If the user's Platform Preferences for Partition is set the set value will be used for both the prompt window you displayed as well as the application, unless it is changed.
If you do not want the user's preferences, specify Partition(Y(), X(), Ignore Platform Preferences(1) );
If you ignore platform preferences, you will need to modify the script below and assume the default minimum size is 5.
Here is a script to capture if the user set the preference from the Preferences UI or Partition UI.
Names Default To Here( 1 );
dt = Open( "$SAMPLE_DATA/Iris.jmp" );
obj = Partition(
Y( :Species ),
X( :Sepal length, :Sepal width, :Petal length, :Petal width ),
Informative Missing( 1 ),
Minimum Size Split(3)
);
obj << split best(2);
//since you are letting the user do this, grab the window and get the script
scrp = (obj << get script); //if the minimum split size was set, can parse it from the script.
for(i=1, i<=narg(scrp), i++,
_tt = Arg(scrp, i);
if(Head Name(_tt) == "Minimum Size Split",
_sz = Arg(_tt,1);
Break();
)
);
_ppsz= Arg(Arg(get platform preferences(Partition(Minimum Size Split)), 1), 1);
if(Arg(_ppsz,1) == 0 & Is Missing(_sz), _sz=5,
Arg(_ppsz,1) >0 & Is Missing(_sz), _sz=Arg(_ppsz,1)
);
show(_sz);