Interesting, I went through a couple of outputs from running the PND, and noticed that there was no messages saying that the game was saved. When starting the games, the emulator always loaded something from the backup folder, but there were no save files in-game. States worked fine.
However, I tried it out in a very simple manner; opened Sujin Taisen, made a save file, did one puzzle, saved the state and quit the emulator. I checked the output, and this time it had indeed written the save in the backup folder. When I started the emu again, the save was there. Peculiarly, my savestate didn't work fine at first; I had to switch the state slot back and forth once to actually load my older data (which I had played already to some extent and then saved to state in fear of losing progress).
I did a backup on the old state and deleted the save data for the game in the backup folder. It still loaded the data with one puzzle solved from the backup folder - the same data which I had just deleted. I then loaded the state with the one puzzle solved, solved another one and then quit the emu. Started up again and there it was - a save with two puzzles solved.
The states don't seem to be causing anything funny since the emu loaded the game I had saved after loading a savestate fine. I find it odd that in the output before I did this test, there was no indication of saving to the backup folder - only the states had been saved, whereas now both were saved. It's also odd how the game loaded the saved game, even though I deleted it. Except for that, I got consistent results (on Sujin Taisen, at least). Well, except for something..
I did another test on deleting the save data to see whether the game again loads it from apparently nothingness, for the sake of consistency in this message. This time it didn't load the data which didn't exist, as assumed. I loaded the savestate with one puzzle solved and returned to the menu. Despite me just loading a state, in which I had saved data, the menu showed only "New Game" as an option - as expected, since the game didn't save in-between. However, I loaded the state again, proceeded to clear a puzzle (the previously cleared one was there), and still the title only showed New Game. The game does save after clearing each puzzle, I'm positive.
The output file has a line with "Loading backup file /mnt/utmp/DraStic/backup/Sujin Taisen (J).dsv" and a line "Saving backup data file," (unlike the file from when saving didn't work) which leads me to believe that there would be a saved game. There's a dsv file in the backup folder. But, upon restarting the emu, the title still only shows "New Game." Any ideas..? I suppose I'm fine with only using states, but it would be handy to actually have the saves work as they should; also, the day when I state save instead of loading without a recent backup is sure to come at some point...