Gas Gas has always advertised that they ship with a 38mm carb, which leads me to believe that they were having supply issues with Keihin. You also have to remember that there was the Tsunami in early 2011 which likely impacted on parts and availability of components from the factories. I know its defintely bumped prices on certain suspension components.
From their eyes, I'm sure it would have been more important to fill the orders for the larger players first (simply supply and demand), and also that Gas Gas factory didn't have a lot of extra coin to be making the demand, I think they took what they could get their hands on. It wasn't an ideal solution, but sometimes you have to take what you can get.