Ah, that's a bug. Sorry about that. I just uploaded a build that should fix it — but let me know. :)
Just wanted to update. It is still stuck. I can activate abox, then press play, it then resets the last box. Meaning after i active and then break a box it will repeat the animation of unlocking the final box with the text repeating. Hopefully that is some useful info/makes sense.
Edit: I also notcied another bug. If you scroll the wheel on your mouse upward consistently, it will bring you back to either the last activity or last save. It brought me back to the mini game after I completed all the boxes.
Edit 2: it only does the scroll wheel bug after I "complete" the final box.
Hmm... I am unfortunately unable to replicate this bug after trying several times. In order to see that text, the game has to have hidden the Logic Train — so I'm not sure what's going on. The "re-unlocking" the final box you described is fine, I don't think that would be causing the issue. What you can do for a quick fix is to restart the game and pick "Amateur Sleuth" mode, then jump to a save before the final Logic Train. I will keep looking for what could be causing the bug.
The second bug isn't a bug — I want people to be able to use the scroll wheel to rollback text :)