I installed a flow thru humidifier two weeks ago and the humidity in my house is still quite low. My house is 2500 sqft and the humidifer is rated for up to 3200 sqft @ 12 gallons a day. Although my house is only a few months old, we are finding it quite dry and the hardwood is starting to seperate. I figured that new construction would take a few years to dry out but I appear to be wrong.
Answer:
Take photos (and good ones) of the flooring because this is just the beginning. Imagine what's going to happen three years down the road. In a house that is less than one year old there is far more atmospheric humidity than hardwood flooring could ever absorb. Your humidfier setting should be somewhere between 35% and 50%. If your house is too dry, you might want to set it higher than that until such time as condensation starts forming on the windows and then you can lower it again. By what you describe, this is not going to help your hardwood floor situation though.