At first I thought it might just be that when the move too fast they miss the collision, but it even happens when they're not moving very fast at all (e.g. when I just drop the box from about a meter off the ground).
Through trial and error I managed to narrow it down to being reliant on the size of the boxes. If I make them bigger, I don't get any of these problems. They're not particularly small though to begin with though, about .5 meters length, and .2 meters width and depth, well within the size range that Bullet assumes for moving objects. Does anyone have any suggestions for how I would solve this?