This is normally from the seal between the glass being broken. If your windows were put in using putty its possible that the linseed in the putty has eroded the seal. It might be best to get new d/glazed units, then get a competent carpenter to install them using the proper fixing compound.
If it was my extension I`d be on to the builder till I got satisfaction, I`d have thought that d/glazed units would be good for years.