If I remember correctly JMP16 did have some bugs with the limit selection IF you had missing values (it might have gotten fixed in maintenance updates, but I don't remember if that did happen). Do you have specification limits set as column properties? You can "solve" this issue (or maybe an extremely annoying feature?) by scripting.
(I will be presenting tomorrow in Finland JMP User Group and something related to this is one small part of it.) Script below might give some idea what you could possibly do BUT do verify that it uses correct limits.
Names Default To Here(1);
dt = Open("$SAMPLE_DATA/Semiconductor Capability.jmp");
collist = dt << Get Column Names("Continuous", "String");
varchar = dt << Variability Chart(
Y(Eval(collist)),
Model("Main Effect"),
X(:SITE)
, invisible // might make execution faster
, << "Gauge R&R Report"n(1) // message could also be moved here
);
dt_gage_results = Report(varchar)["Variability Gauge Analysis for ?", "Gauge R&R", Table Box(1)] << Make Combined Data Table;
-Jarmo