This problem occured while testing Mystic Quest (Germany) aka. Final Fantasy Adventure (U) on r810 of VBA-M on Ubuntu Linux 8.10. It appears to happen with any region of the game. The game itself works perfectly.
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When using the save function of the game, it appears to save the progress on one of two available save slots. Upon restarting the game or VBA-M, all previously saved progress is lost. A save file with the size of 256 bytes has been created but it is completely filled with "FF"s. The save type is set to automatic.