Generally speaking, A-Shell, like most other Windows printing programs, establishes and maintains it's own settings, independent of those that may have been set manually or by other applications. The duplex option would be one of those settings, and it defaults to OFF. So you probably need to either add the
//DUPLEX (GDI directive) or the
DUPLEX to your ATE-side printer init file(s).
Side note to the documentation department: it could probably be made more clear that the default is OFF.