I know a lot of hardwood manufacturers of pre-finished floorings use putties to fill small imperfections in the wood. Did you buy this prefinished? If so, there's a chance that could be putty that was used during manufacturing that was stained to match the floor much better in the beginning, but...
Filling gaps in solid hardwood is a tricky business. Timing is critical. Gaps showing up in the winder, or during dry seasons may just be due to natural shrinkage of wood flooring when humidity lowers (like because of forced air systems or dryer climates). Filling these in can cause problems in...