I'm in a 100 year old house and I believe the floors are original. They don't seem to be tongue and groove, but just flat boards nailed into the subfloor with finishing nails.
Periodically, the nails start to inch themselves up. We hammer then down but they just come up again. This happens all over the house.
Is there a way to secure them more permanently? Replacing them with different nails? Coating them in some kind of adhesive?
If I understand correctly, you have small-head nails driven through the flooring planks vertically and flush with the surface. They're working upward from the up-down flex of the boards as you walk.
I would acquire a nail set the correct size for your nails and drive them slightly below the surface of the flooring. This will serve to lock the nails into the finished floor, and any movement will occur in the subfloor instead. You could then use a colored nail hole putty to hide them.
Another solution would be to pull the nails with a needle-nose plier or other similar tool and replace them with slightly longer, larger, or ring-shank nails to give them a stronger grab.
Most likely the nails that are working their way loose are smooth shanked and will continue to do this no matter how many times you "set" them.
This occurs due to ,not the nails moving, but the floor planks moving the nails. Changes in temperature, humidity, and vibration all exert forces that make minuscule adjustments to the planks and ultimately the nails.
If aesthetics allow you could either replace the wayward nails with a finish nail that has a more positive "lock" in the wood. Any ring shank or spiral shank type nail will hold more aggressively than a smooth shank. If you have access to the under side of the floor consider screwing up into the loose boards with an appropriate length screw.
If you'd rather not have counter sunk nail holes showing fill them with an epoxy type filler otherwise the standard wood putty filler will eventually break loose.
