OK, so let me understand this. You turn up at 90 minutes, which is actually 60 minutes and NZ tell you check in is closed but they will re-open it for you and you make your flight? I have frequently checked in at SYD at 60 minutes and ex WLG frequently at 45 minutes and had no issues making general boarding. To me it seems like the issue has been solved, NZ let you on the flight, no one was left behind and it serves as a good lesson when travelling with clients (or in general) to always recheck your departure time on the day of travel.
Now if you are saying you got no notification at all and had supplied valid phone number, email address then I would say the integration is broken between Virgin and NZ IT system and that could be on either airlines side. That is something worthy of bringing to their attention so they can troubleshoot and get fixed.
Out of interest I see you are NZ Gold Elite, why didn't you book directly on the operating carrier in this case? For these sort of reasons I always try and book with the operating carrier where I have status with them as they generally look after you far better when things don't go to plan.