Problems with Pocket SNES

[Kolano]

Yes, if you were poking at your extended rom then there is a good
possibility it's been unlocked generally. PocketSNES may be confusing
it with your regular storage card. In some programs you can reselect
the appropriate location and have things work out, but certain others
are just a bit incompatible with extended rom being unlocked.

You might also try copying the roms to the extended rom, though think
you'll likely only fit a few.