Thats cause I didn't enable memory paks (in controllers) for this version (meant to.. probably will switch it over when next gles plugin comes out. As of the moment by default only saving onto the cartridge is available. If you remember the N64 you could have very small saves on the N64 cartridge (eg. Zelda) whereas others required larger saves that required a memory pak to plug into the controller. To enable the memory pak:

In a new terminal, open blight_input.conf:
leafpad .mupen64plus/blight_input.conf

You'll see on the third line: plugin=1, change it to 2. (Also note: 5 is rumble pak.. but it only works with a Logitech gamepad at the moment.. and thats only if your running mupen64plus on PC)

Save and exit... and your done.