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 :)