H bozzer,
sounds as if you have fungi caused by the decaying wood material left after the tree was cut down.
Sorry to say, but the only real way of getting rid is to remove all the soil from the area, and replace with fresh, sterile soil before re-seeding or turfing. The fact is similar to the couch grass/bind-weed problem, if the smallest bit is left in then it will return.
I did forget that the roots and all dead woody material should be removed but this would happen if the area was excavated properly.
Hope this helps,
Bryan.