Several points.
1. Just because E class does not show up as an eligible booking class for international flights does not mean it does not exist; it does.
2. E class, confusingly, is eligible for DOMESTIC bookings as an earning class - so the MEL-SYD example above is fine
3. I think it is a fair assumption to make that the ticket booked would earn given QF do not, as a rule, have classes of revenue bookings that do not earn under QFF (but do not under other schemes, of course)
4. The screenshots and comments about the booking screens include the word "MAY" a lot. ie QF is clearly saying "QFF members *MAY* earn up to...." but does not guarantee it. That's their get out of jail card there should they wish it
I think the agent who suggest it was an employee ticket was simply going off maybe what other uses of that booking classes were, but perhaps for this particular discount/sale fare it was booked into E by either design or error.. the original fare rules would need to be consulted if QF intended it to be non earning or not. By QF's posted earning rules, E class does not earn on international sectors. Confusing because it does on dom. I'd still follow back up with QF on this one, but I think the OP is out of luck if it did book into E for whatever reason.