Issue with game not saving what shines you collected on shine select screen #3

After just starting a new game on version 3.1 I went a entered Bianco Hills Shine 3 (The Hillside Cave Secret). It turned out to be Noki Bay's Red Coins in a Bottle mission. After going though the dialogue and entering the bottle I then went to the Shadow Mario chase level in Bianco Hills. However after knocking him down and collecting the rainbow shine sprite when I went to enter Bianco Hills again to do the next level, I realized the game didn't save that I beat Bianco hills Shine 3 and that the shine is still blue on the shine select screen. Seed: 68977915