I have no trouble with playing this game with my M3 at all, yet I have found a strange issue with the actual game save. I orignally started playing Diamond because it was the first of the two roms that I downloaded. About one hour into Diamond, I had decided to load up Pearl and just made a new game.
Something strange happened when I played Pearl. It had the same savegame as Diamond. Now with the M3 it should have created a different game save .dat file for the new rom. It had, but at the same time, Pearl was loading up the game from Diamond. (??!!)
Now it seems I have managed to get a persistent save game with either Diamond or Pearl. I'm trying to get rid of this, but I can't make a new save.
Regarding the M3, I know about how it will store the last played gamesave until you reboot the DS. So after rebooting the DS and making use the the M3 had written the gamesave to the SD card, I proceded to delete that save and start up Pearl again to see it nice and empty. It didn't happen, my character and save were still there.
A list of things I have tried to remove this gamesave have been,
Format of SD card.
Booting the M3 with a different SD card with only one rom (Pearl) and an additional blank saver created via the game manager.
Using the game manager to write the games to the formatted card once again (both Diamond and Pearl, which should have and do have individual save files). Upon loading either Diamond or Pearl, the same save file still exists.
Renaming the roms before writing them to the SD card to create a unique save file.
Updating the M3 with updagcsd.e28 firmware, downloaded from the M3 website, again.
Installing the M3 game manager, again.(for no real reason).
Removing battery from NDS to clear saved data from the actual handheld itself.
Starting either Diamond or Pearl again, and using the Report menu item to save the game again will not work.
Loading the orignal stuffed up save file and using the Report menu item will save the game, but after rebooting the NDS and loading either Diamond or Pearl it gives an error message about 'not loading the report, and will read the previous report'.
Any ideas? Or, other people with M3's, what happens when you load up the different version rom to yours, does the gamesave show up in the main menu? Whats up with my M3 here.