I cannot rememeber, which version of the BAT printed in double side mode correctly. But actual version of TheBat! Professional 9.2.5 32bit and some older ones not remember double side print mode settings and print the mail pages on separate list of the paper.
I don't think so that this is thing for TheBat settings. You can setup double-side printing in your printer settings (button "properties" in TheBat print dialog).