Hi! There are 4 boxes at the moment. But 4th is unreachable if you are playing in sandbox mode. On map you can see where they are and how many
Ok so, there is a glitch with the boxes and it has nothing to do with the sandbox as far as I can tell. My first playthrough I never got the spanking idea. I thought I was just missing it so I kept playing until I did every scene except for the dog mask and still didn't have it so I went back to the breakfast scene because you have noted there that that scene has two boxes available. Yet no matter what I did I could not find another.
I then thought since you have transferred from a sandbox to a world map system maybe something was getting lost because of the progression path I took.
When I first played as soon as the game showed me I could pick up three boxes right off the bat (MC room, yard and hall) without really having to do anything of course I immediately picked all three up and opened them. I believe this is the issue.
I restarted and picked up the three boxes again right from the start and then when I opened all three this time I paid attention and noticed the first two boxes I opened both gave me a submissive idea but when I opened the third box it gave me nothing, it just disappeared. All I had in inventory was the two submissive ideas.
So I restarted again but this time I picked up only one box, opened it, and used it on a scene before picking up and opening another as I needed them and this time I got all four ideas in a few minutes of fast forwarding.
I believe since the third one gave me nothing the forth box gave me what the third should have and left me unable to get the 4th idea (spanking).
Hope this helps.
