Of all the posts, Firecrafter is the first that identifies the issues without implied indignation. Whether the scoutmaster is "right" or "wrong" is immaterial with the information given. As with all things, there are two sides to every story. As a high school teacher and adult scout leader, I have come to understand that an adolescent mind does not understand things the way adult minds understand them. Teenagers are often reluctant to tell there parents of any negative parts they play in a situation. Having said that, it does sound like your son is going about trying to change the situation the right way (with respect for the committee and Scoutmaster.) Take Firecrafters recommendations to heart.
It does not sound like you are involved in your son's troop. If not, why not? Most young men who make Eagle, get there only from the support of their families (parental involvement). If you are involved with the troop, congratulations! Now go talk to the SM (also in a respectful manner) and find out his side of the story with an eye on resolution. (Again Firecrafter is right on)
These forums are good to get things off your chest, but generally bad for solving problems. Your energies might be better served talking directly to the SM rather than listening to some of these posts. Remember to "Run the 12" (mentally go through the 12 points of the scout law) as you talk with the SM.
I pray that your journey is a successful one.
Proverbs 13:10