My son was experiencing the same thing. I believe we tried to potty train him a little too son. We potty trained him before my daughter was born. She was born a few months before my son turned 3.
Here is what I did: made sure he drank water (1/2 of his body weight in ounces), good roughage food (including fresh fruits and vegetables--not too many bananas as they will constipate him), basically try to stay away from foods that bind (ie peanut butter, cheese, etc). My son was so bound up, and he would not let us give him any more laxatives or suppositories, that we took him to the doctor and she had to physically remove stool from his bottom. It was horrible for him and it really hurt me to see him go through that. The doctor then said to give him Mineral Oil (yuck!). I tried and then thought if the Mineral Oil pushes the bad stuff out it must push the good stuff out too.
So I switched from his Flintstone vitamin (which can bind up a child) to a food based Multi Vitamin (Ocean Wonders) and gave him a Probiotic (Optiflora). At his follow up visit, the doctor said the supplements were great (she copied down all of the ingredients and wrote them in his file) and said keep him on them.
Hope this helps. If you want to know more about what I give my son, email me at ____@____.com Beth