Lasiorhinus,
The total cost of the card is not only for Auscheck clearance but also for the printing of the card and the time and effort taken in processing the application by the issuing body. The high cost of printing the card can be directly attributed to the fact that the printing equipment costs in the vicinity of $40K.
You are correct about the clearance payment. It has to be paid whether a clearance is granted or not. Sort of like a dealing with a bookie at the racetrack.
Stats for clearances being declined for ASICs are relatively low.... compared to those applying for MSICs.