are you using the akaio 3-in-1 options or gba exploader?
for akaio 1.4:
start > 3-in-1/fas1 > Prompt before Save/Load set to ENABLED
for gba exploader:
in the ini file remove the # before the last line about saving.
the cart will now prompt on boot up to back up your last save. otherwise just follow the on-screen information for what button to push to back up your save.
as for your 3-in-1 assuming the battery works fine, your saves are stored in the sram. the sram is shared between the psram and nor modes. if you flash over a new game before backing up your save, your save file will be overwritten. gba exploader will keep track of what save was last used for each mode, but that does not mean the save is still in sram and can be backed up to your msd.
give those options a try and post back.
-another world