My friend has a 3 year old and when she started potty training he did exactly the same. She would find him sitting underneath the table on the floor, or he would be playing with his brother and then suddenly just sit down - holding it in. He would sometimes not go for a number two for nearly two weeks. This went on for about 6 months. He was dry with number ones, but number twos was completely differnt.
She finally took him to a specialist to see if anything was wrong. They say that he is physically fine and that it is a mental issue. He is now on medication to make his stools more soft and it makes him go at least twice a day! He is back in pull ups and he has to stay on the medication for at least 3 months - it will be reviewed then.

Not sure if this helps or not, but at least you know that you are not the only one with a problem.

xx

Holding down emotions perhaps? I would give him diaper to poo in. Some of them have a hard time letting go of doing it in the diaper and take their time. Don't worry. He would get to it.

The Mother magazine has a fabulous article about toilet training a few issues ago. You may want to look for it.