My DSi has the same problem.I don't know. There's no reason for it to have broken. I noticed that it was messed up while playing SMT IV where the the R or L button allow you to see info on demon moves. L worked fine, but not the R button. I bought the 3DS around September of last year, so it's unexpected that I'd have this much trouble so early on.
Haven't found a solution yet because I have a 3DS now.