I've tried replicating this bug based on your instructions, but I can't seem to force it to happen.
Could you try deleting the save folder altogether (C:\Users\***YourNameHere***\AppData\Local\CHSr012) and see if it still occurs? Maybe you're loading a save from an incompatible version that's causing issues.
EDIT: Are you trying to save/load with mouse or keyboard controls?
Using a mouse to save/load.
Deleted my save folder, lemme go step by step as a just in case thing:
Clicked through intro, named self Dipdo.
Clicked Guts option.
Clicked "Sorry, wanted to go somewhere silent."
Clicked "Make a game of it."
9/7 Monday Afterschool, saved on 1st, 2nd, and 3rd file, in that order.
Closed game, opened game.
All three load, so far promising, let's push it a little more in just in case.
Spend Time with Twilight, click "I was hoping to follow your lead and study." then "Ask what's bothering her."
Save on just the first file, close game, open game.
Clicking on first save causing game to sit at title.
Clicking New Game now loads first save.
