I have a natural cherry hadwood floor and have similar problems. They filled in the inconsistent places between the boards with putty and the putty is breaking out. I hear the floor make cracking sounds throughout the day, even if I'm not on it.
I was thinking about getting either a humidifier or a dehumidifier. Does anyone know which would work better of if either would work at all. It seems plausible that if you at least try to keep the humidity consistent, it should help.