Sounds like either the smell remained even after all that cleaning (you might need to try something to kill the scent such as vinegar/baking soda mixture or one of the good enzyme-based cleaners) or he has a reason why he feels he must do that such as marking the place. (dogs use either urine or poop for marking)
What do you do when he does it outside, does he get praise and reward(s)? What do you do when he does it in the room?
Is it one particular spot in the room or any area within?
I remember Dr. Coren had some good suggestions on redefining the area. Such as using the area in question for feeding and/or play with the argument that dogs don’t potty where they eat or play. You could definitely try that.
This puppy needs surgery. Call your vet NOW to discuss this.