Try this:
Go to Options > Game Boy Advance > Configure. In the save type tab make sure the save type is either set to automatic or flash and the flash size should be 128K.
You might also check the game overrides tab (per game settings, available when the game is running) and make sure that they are either all set to default, or RTC: enabled, save type: default or flash, save size: 128K, mirroring: default.