I fiddled around with it last night and it's actually working again. I tried uninstalling and reinstalling the WinTV8 app, which also included all the drivers. That didn't work so I tried physically moving the card to another PCI-e slot and that didn't work initially, but then all of a sudden it appeared in the devices list in WinTV again and was able to scan up the channels - and goes without saying it's working in NPVR again.
So I'm still not entirely sure what was wrong, but I guess I'll monitor and see what happens next. Maybe the card is on the way out if it seems to be working one day then not the next, and vice versa.
Any thing in the filtercheck log that looks out of the ordinary?
AMD A8-3870K 3.0GHz (onboard ATI HD6550 graphics), 8GB RAM, 500GB SSD + 500GB Hard drives, Hauppauge Colossus 2 (HDMI), Hauppauge WinTV-NOVA-S-Plus (DVB-S), Hauppauge HVR-1200 (DVB-T), Windows 10 64 bit, NPVR 3.9.2, MCE Remote/IR Blaster, IR Server Suite blasting to SKY TV (NZ) OnDemand set top box (Kaon NS1120).