Some time between version 3.41 and now that seems to have happened. I can't find it listed in any patch notes so I assume it is a bug. I have confirmed that opening up the same save on the older version has the pervert menu correctly populated with only unlocked scenes, so the save itself is at least safe.
Might not be in the public patch notes then. Unfortunate, since I prefer unlocking all the scenes over time. Hopefully the option to go back to that method is added in the future.
