Steve the way the system works is when you got married there are four copies you signed We took them to the registra who stamps them
One copy remains there one goes to the NSO from the registra, we paid an extra hundred piso for a taxi
to get it to the NSO for fast on the system
One copy goes back to the Priest who made the 4 origionals you signed and the last with the registras stamp on should be with you
If it failed to get to the NSO and it can take 3-6 months shouldnt though then I would get your Missus back to the registra with your copy and a couple of photo copies and see what they say
In our case Cebu we registered on 1st March and were told by the NSO (called them) that it was on the system so we ordered 4 copies on the 21st and should get them on the 31st