Hello T.,
Actually, my big concern is that you said he normally has a BM every two or three days. Even though you think he is not constipated, this is not normal. A healthy person should go 2 or 3 times a day!!! He is in need of probiotics and perhaps even digestive enzymes. That might solve the other problem that you wrote about.
Three years old is a bit young to be having these problems. Be sure he is drinking enough water (not including any other drinks-juice, soft drinks or soda, anything else doesn't count as water) and getting enough fiber.
If you want any information on any of these things, just get in touch with me. ____@____.com
I hope everything works out and you get to the bottom of the causes. Water and fiber are really important.
Good luck to you and your son,
C.