That's odd, I've never had anyone report getting stuck on that before :o Usually it's the one bad end that gets completely missed cos the requirements tend to be met to pass it almost by default.
You're correct that you get the good ends when you get the letter at the end of each route, yeah.
Did you reload saves at any point when completing the original 5 routes? Like with counting bad end points, if you go through a good end, and then reload an older save to pick a different route, the good end point won't register.
So for example, if you are at bad end 12 now and you reload an older save to go get good endings of the other routes, then save and reload back to your save at bad end 12, that won't count those good end points, and you'll remain stuck at bad end 12. If you were missing any good ends from the original 5 routes, you'd have to get them and begin the ??? route again on the same save.
Did you get both good endings in the gamer route? It's the only one of the 5 initial routes that has 2 good endings instead of just 1.
Also, are you missing anything in your gallery from the initial 5 routes?
Just so you know, I'm gonna head to sleep now cos it's almost 3am here. If you can't manage to get past it, I can always send you a save file when I get up in the morning that will bypass that bad end for you if you want :3 Just lemme know what name you entered for your character.