CVSNT is a drop in replacement for CVS so they say 🙂
Well ish…  To cut a very long story short I had a problem very similar to this one. I had removed my old CVS install and installed CVSNT in its place.
I go to a dev machine, use WinCVS and BANG no such repository!  I run to my desk and ssh into the server, no all our code is there and still in the same place and no change to the CVSROOT on the dev machines either.
Fast forward a few hours of keyboard bashing and searching…
Even if you are only accessing CVS via SSH you will still need to configure /etc/cvsnt/PServer just copy the PServer.example file to PServer edit the Repository0 section to put the path to your repository, save and you are done 🙂
This is a CVSNT security measure apparently and it could have been mentioned a bit more prominantly IMHO 🙂
Hope this saves someone else a lot of time and dry cleaning bill 🙂