Flight was Air New Zealand operated by Virgin Australia
Flight No: NZ7942
Fare Class: Seat + Bag
This is all that is on my Flight Centre Itinerary
So that explains the VA boarding pass. And VA boarding passes do show fare class.
I have to say that it's weird for VA to have put an incorrect fare class on the boarding pass - and I suspect that's why they caved in and offered you something. However, it seems like NZ fares booked through third party sites routinely book into fare class X, in which case it probably is true that you purchased fare class X. Overall though, I think VA should have just given you 0.5 points/mile on the basis that they printed a fare class on their own boarding pass that suggested you were entitled to 0.5 points/mile.