We had that problem at one time and later discovered a forgotten sack
of potatoes in a rarely-used cabinet. Best estimates put them at
upwards of 3 months old at least, and they had decayed into a black
liquid. The smell was incredible, but only once we opened the cabinet.
Miraculously, teh flies disappeared after dicovering and removing the
black liquid. The moral? Perhaps there is a hidden rotting something in
your house, where the flies are eating and reproducing.