You should be able to pre-allocate seats on QF international flights (flight numbers QF1-QF399). If your agent won't do it, then call Qantas yourself. You cannot pre-allocate seats on QF domestic flights - this is done automatically based on FF status and preferences registed with the QF FF program.

The only limitation to pre-allocation on QF international services is that they will only pre-allocate up to a certain proportion of the economy cabin so allow for some last minute flexibility with families/groups at check-in time.

In my experience, I have been able to pre-allocate seats in CX economy class as well.