Mupen64plus save problems

I've been playing a game and I got fairly far along and have saved every chance I got but for some reason when I close out mupen64plus on my sheild tv and go back to the game it starts me back close to the beginning. It's happened twice now and I'd like to know what I'm doing wrong. It's happened with 2 different games. Paper mario 64 is the game that's the biggest issue. It doesn't even start me at a save game area, just some random spot talking to a random character. Is there a setting I'm missing?

what with your OS did you have full rights as administrator and how you create save save slots or direct save as