I am also at a university - when we switched over to All of Govt (accessed through Orbit) I recall AP were not earned for a short while. Now we earn as as normal on AirNZ flights.

I don't really have an issue with economy on work flights - but may change my mind as my university is cracking down on 'claiming' any days that are not work (previously I arranged a day off for recovery). And then there is a university goal to reduce air travel by a third - but that's a separate battle!