There is a possibility that the overlay gets injected in the "wrong" window. For example when your game has a launcher which for itself has its own render surface (which hooks in the overlay). Then it could happen that the actual game window will not receive the overlay injection.
From my experience this is rare. I even created a multi viewport application with Steamworks.Net and the last created / active render surface always got the overlay injection correctly.
But I experienced that when the back buffer has a different size than the actual render surface, then the overlay can get stretched and distorted; maybe even invisible if the true render area is to small. This is something which could happen in editor environments but I did not see that so far in games.
Did you try the "Hello Steamworks.Net" sample from the repo? You could build it for windows, add it to steam and see if the overlay works. If you don't have problems with the overlay in general, then this will work.