I started playing Fallout 4 a few days after it came out. A couple of weeks ago, I decided to start a new game. When I saved the game and came back to it the next day, I was happy to see that there were two separate profiles, one for my level 30 character, the other for my new character(both profiles had the same name).

However, today, when I went to save my game, I noticed that there was only one profile, with saves for both of my characters under it. What happened to my second profile?

This should be pretty obvious. You most likely confused it by using the same name, so it just thought they should be under the same profile.

Well, for some odd reason I could only see the profile I was using, even when I quit to the main menu. However, when I quit out of the game and restarted it, I could see both profiles.