Considering the box came out of a flower, my guess is that it contains... a seed! Maybe to grow more trees of harmony?
What that pokeball actually was refering to was a device to lead up to revealing Celebii, but they gave up on that plot point without ever getting to the big reveal. They dropped it leaving many people for years wondering what that was all about. On another note I don't see not worrying about the box as an inconsistancy or even a concern. I feel that Celestia essentially applied something along the lines of: you won't know now but the answer will come to you in time Twilight, have faith in your friendship. Given that, and the fact that nothing has popped up as a lead related to it I think it makes sense that it's not actively being tracked down. So I disagree with the top post but for a different reason. Also I definitely think they are getting to it. Also if you didn't see McCarthy was being smug about the thread: http://1.bp.blogspot.com/-7Z9F_eBHXS8/UsiDtk10jfI/AAAAAAAAMIE/cIWOpaCHqjw/s1600/Capture.PNG so we know it's something. ^_^
