Unseen Application

I was in the game, and I was in a queue, so I was watching YouTube on the same computer as I was waiting. When I went back into the game my mouse started not working, so I had to restart the game. When I tried to do this it crashed. I tried again and when I got into the launcher and pressed play, it said, "Already running in this game directory," and "Already joined the game as this user," so I did what it told me to do, which was create a new installation in a separate game directory. When I did this it still said that I had already joined the game as this user. I couldn't do anything other than just get in the game, since I had no idea why it thought that I had already joined the game because I wasn't in it at that moment in time. When I got in the game I added the server that I was playing in before in to that installation. I tried to join but it said it was in an invalid session. After contemplating my problem I decided I would just uninstall the game and then reinstall. When I tried this it asked me to close all applications of Minecraft launcher. I was confused and helpless because I couldn't uninstall, and had no idea why it thought that there was still an open application of the launcher. I hope you can fix this somehow so that I can play Minecraft again.