Hm, I can't replicate your problem which means it's probably one of three things.
1) You didn't actually get the submissive good end, you got a bad end, but most likely you would be able to tell, if you "levelled up" afterwards you got a good ending of some kind.
2) You aren't looking in the right place. You should go and talk to Naughts and Magellan again and click on realistic masterpieces, it should show up under that.
3) You uncovered some kind of bug, the game tracks what levels you complete based on binary variables but those can sometimes get messed up unintentionally. Looking through, I can't identify any issue myself, but I miss things sometimes. Let me know if the problem persists and I'll try to see if I can find anything.