Answering to your edit, MJC, I can see that this is the most of a conundrum I have seen in my life. My new conclusion: It may be both your cartridge AND your 3DS causing the issue, as the evidence you described is not only a cartridge acting up, but a 3DS acting up, too (you would not believe the amount of 3DS' I went through that had the problems' your 3DS (not the game) is having right now). All I can say is that either get the 3DS fixed or buy a new one, as that's the only help I can give to your situation. Sorry.