Ah, interesting! That level is the first one that really tests the player to see if they "get" it yet, and it seems like we didn't do a good enough job at explaining because a couple of play testers got stuck on that same level.
The trick is to stand on the square, throw over the river, and then play as the other character, catch the box, and throw it back. Then you go back to the first character, throw the box over again, and then wait for the second character to throw it back.
The timer is an unfortunate necessity. We're storing 60 frames of input data each second for each player, and so we need to limit the number of seconds in order to not go crazy with memory. Those earlier levels could have more time though, you're right there.
Thanks for playing! :D
(-Joe)