@mitu I just figured it out moments ago after a lot of testing this morning. I have a third party music player that fades the volume before starting a game. I think what happens is it fades the system volume to fade the music before starting emulation. Then, when returning to ES, the System Volume remains what it was faded to prior to emulating the game.
This can be marked as resolved. I'll report this bug to the creator of the music player. Thank you!