Yes, we had a similar situation with our son, who just turned three. We didn't realize it was the milk until we took him off of it, and he started sleeping through the night. Before we tried removing milk, he woke up several times a night and only milk would put him back to sleep. Once we switched to soy, then later almond and potato milk, his sleep improved greatly (and so did ours!).
We took him off of milk because we were looking at possible (now confirmed) autism and going casein (milk protein) and gluten (wheat, barley, oat protein) free is a dietary intervention for kids who suffer from stomach distress or behavior that might be correlated with diet--and these are often common side issues for autistic kids. I don't know if your son is showing any developmental delays, but ours was--only a handful of words at 29 months, not putting two words together, etc. I'm not by any means suggesting your guy might be autistic, but you might want to look into what moms are doing with the Casein Free/Gluten Free diet to see if the gluten might be another issue for you. Or maybe, you're just getting some extra behavioral issues off and on due to hidden sources of dairy that he may have inadvertently eaten. French fries from many fast food restaurants have milk products in their coatings, for example!
If you want to read more about the gluten free/casein free diet, here's a great website (it's from a website for autistic parents, but don't let that put you off--it has great info).
http://www.tacanow.com/dietinfo.htm
Let me know if you have any other questions about going dairy free that I can help with. It's a bit of a pain sometimes--but so worth it when it helps my little guy so much!