It is per shipment. The way it works is that the value of the shipment + shipping must be less than AUS $1000.
I've never had any problems with this "formula".
I have a friend who works in Customs Clearance and he told me they CAN keep track of shipments and if you were importing less than $1000 worth of goods every week of the year, it will spark their interest. If you imported several packages from the same source, on the same day, then this can also raise a red flag.
You should be ok Pete.
