Maybe you need to activate the workbook between each plotting. e.g.
plot_gboxindexed irng:=[dataSheet$]Sheet1!D group:=[dataSheet$]Sheet1!A theme:="Box_Data in Line" rd:=[<input>]<new name:="Voc">;
win -a %(dataSheet$);
plot_gboxindexed irng:=[dataSheet$]Sheet1!E group:=[dataSheet$]Sheet1!A theme:="Box_Data in Line" rd:=[<input>]<new name:="Jsc">;