DISCLAIMER: This happened a while ago so it may have been patched or something whatever Damn, good to be back. Anyways, a while ago, I got a N3DS and both of the N3DS exclusive games (Binding of Isaac and Xenoblade) and I enjoyed it quite a bit. I got it I think around June-July so I've had it for a bit. A few months later, a weird glitch happened. So I was trying to enjoy some casual Isaac, so I booted it up and I was welcomed by the title. It was a bit laggy-ish so I just brushed it off. When I got into the game, there was a FUCKTONNA LAG. Like, seriously, it didn't go past 5 fps. I moved around a bit and messed with the controls, they all worked fine except for the C-Stick and Zl and Zr buttons, well I have no idea what they're called they're the extra shoulder buttons on the back. Anyways, they didn't work. I had suspicion so I booted up Xeno and it went relatively well. Well, except for the fact that I couldn't use the C-Stick or back buttons, so I shut off the console and then everything was lovely once again. It's like there's some sort of switch for regular 3DS and New 3DS. Again, this happened Sept-Oct so I'm not sure if it's fixed or whatever but it's only happened to me once. Has this ever happened to anyone else.
sounds more like a console problem, maybe a memory issue. I'd assume new 3ds games would check to see what cpu they are booting off, like how GBC games do