Brad_bb--It's not that the pegs have "backed out"--the pegs are literally two separate pieces. The builder was unable to drive a single peg the whole way through the joint for whatever reason (looks like they didn't bother to taper the end to help with the hole offset, possibly). To deal with this, they drove a second peg in from the opposite side, but the second peg doesn't "tie" anything together--it goes to the tenon and stops. It basically is there to give the appearance of a single solid peg but, to my untrained eyes, appears to do nothing structurally. None of our pegs are trimmed flush--they all stick out about an inch or so, which is why I was able to pull the stubby end out and find this in the first place.

But, yes, you are right--I am not a professional timber framer, which is why I am looking for a third-party opinion before I do anything else.