Yeah, it seems to be broken. Doesn't the box reset its position when you restart from the last checkpoint?
I didn't test that unfortunately. This is on the web version, not the download (I don't have Windows), so it loses any save files when the browser is closed. If you want try to recreate it, this is what I did: I moved the box to below that gap, walked to the top of the gap and tongued the box across, moved to just below the switch-activated block and tongued the box to me, then moved two spaces left of the box and tongued it one space, then walked to the right of the box and needled it through the beam. Now I can't tongue it back. I did this before learning that the box stops the switch-activated block from moving. I can try doing this again and then restarting from a checkpoint. But if the game saves whenever the player leaves the area, which doesn't reset the box, wouldn't it just restart at a save-state after breaking the puzzle? In other words, someone would have to know the puzzle was broken and reset before leaving the area? I will let you know if I can repeat the situation. Hope this helps. :)