I'm sorry about your son's diagnosis. My son, Caleb was diagnosed when he was three, he is currently 14.
Caleb's dosing was very low shortly after diagnosis - less than 2 total units a day. The simple answer is lows are a result of too much insulin. A more specific reply to why your son is having lows when he is, is much more complex. Caleb had a very strong honeymoon and it went on for a long period of time. It was hard at times to manage his bg with a pancreas that was still doing some work, but doing so in an unpredictable way.
Even without having to manage a honeymoon period (which also has its benefits), getting dosing right considering carbs consumed, the impact of protein and fat, growth, variable activity - it's very difficult to manage without experiencing out-of-range blood sugars one way or the other.
Is that your question though, or are you asking something much more scientific that I may not be qualified to answer?