How to control when autocash rules are used?

In R11, when processing a lockbox file where the transaction number (invoice) was provided, if the invoice had no amount due, the Post Quickcash program would process these receipts as unapplied, and ignore the auto cash rules.

In R12 following upgrade from 11.5.10 to 12.1.3, the same lockbox definition is run, and where the invoice has no amount due, the program starts to apply the autocash rules.

Dous anyone know how this behaviour is controlled and what the difference between R11 and R12 is?

Many thanks

Rob