Most of the rot problems in houses are caused by dry rot or wet rot (both names for types of fungus). Both generally develop because timber is too wet (although it is worth bearing in mind that timber can naturally be up to 20% water).
They are actually relatively frail organisms which don’t survive well when there are fluctuations in humidity or temperature, so they tend to develop in areas with constant bad ventilation and high humidity.
The likely culprits will be the space between the floorboards and the foundations (if the ventilation holes in the exterior walls have become blocked) and the timbers in the roof (if you have over-done the insulation).
The solution is usually to restore proper ventilation and cut out infected timbers.