leadegroot - 11:57 am on Sep 12, 2012 (gmt 0)
You could try to set the country in webmaster tools (probably won't work - its usually turned off for CCTLD domains)
You could put a canonicalization meta on each page, to the correct url with correct domain.
Basically, I'd say the .au site has picked up more 'strength' than the .nz one and so the .nz pages are falling to the Duplicate filter. It shouldn't happen, but maybe they have put .nz and .au in one bucket? :(