Oh so it seems like a problem on TWL_FIRM, like it's corrupted or something like that, because when you boot a .nds file on TWLoader it reboots your system in TWL_FIRM mode, which is a part of the original DSi console, and try to run the file, but if it's only plain black after the reboot it means that's something wrong with TWL_FIRM on your consoles, have you installed another type of hack on 3ds before arm9loaderhax? like Rxtools or something like that and have instaled a patched TWL_FIRM on that Emunand-Sysnand system?