Similar things have happened in other underwater rescue situations and it almost always turns out to be equipment involved in the search. The sonar bouys dropped by the planes are extremely sensitive pieces of equipment.
If I had to guess, every 30 minutes or so a boat running a grid search pattern would get close enough to one of the bouys that it was able to pick up sounds from the boat. As the grid pattern took the boat further away from the bouy it wasn't able to continue to pick up the noise, and the "knocking" stopped after about 4 hours and wasn't heard again until a few days later. Then the search pattern changed, and boats started getting close to the bouys again.