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.

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.

Env V:
OS: Linux.

Windows not effected (except Vista when using from the Program Files folder)

VBA-M | NGOHQ | Post Impact Productions | TNHW | XBCD 0.2.7

Test to set "don't change batterysav" in File ->Load game.
Then your Batterysav. gets untoutched from Quicksaves.
In other fact an Quicksave made bevor you saved in the game, overwrites the Batterysavfile with owne Data(in your case with empty slots )?

Yes, I knew of that behaviour. However, I didn't use quick saves in this case.