Most likly the smell from the old carpets and any old pet stains had gotten in the gaps, into the wood and under the floor.
Does anyone else but you smell the floor? Some time certin people are far more senitive to certin odors.
Hardwood floors get covered over all the time for one reason or another.
There a pain to keep up, expencive to refinish, cold under foot, there noisey to walk on, old stains ect.