@kibo, there are three MASTER VERs: no dots, one dot, and two dots.
@Joe: go into the test menu, and look at the high scores that are saved. Is it saving scores properly? Do any scores look strange (weird symbols, etc)? First I would reset/initialize any saved scores on the board. Then, I would try and play some runs and get some scores above the default. Then I'd power down and go into the test menu to see if they are saved there.
I suspect the problem with the DFK 1.5 board I saw in an arcade in Japan is that the EEPROM for saving scores got corrupted. So, I wonder if that is what happened with this Futari 1.0, since it exhibits the same symptom.