Load up the Emulator and a ROM and goto Options > Emulation Setup, near the bottom left you'll see 'NDS Cartridge Backup Media' change that to Flash 512KBytes, then hit File > Reset Cartridge. If changing it to Flash 512KBytes doesn't work try changing it to EEPROM 64KBytes instead or another one. After changing the setting don't forget to click Reset Cartridge.
It should work.
P.S also make sure that Reset/Startup Entrypoint is set to 'Start Cartridge Directly' in Emulation Setup.


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