I was trying to get my DSTWO to register on my 3DS and after finally getting it to work I went to play some mario kart. Anyway the long and short of it is that after the game was not playing correctly I turned off the system and turned it back on.

The box to select what you want to open on the menu kept moving right. I had this problem on my wii with my nunchuk before, which was normally fixed by turning it on and off. I also tried holding left on the d-pad to counter it, whilst turning it on. I also tried callibrating the analog stick which failed.

So now I am stuck with the controls completely messed up, sometime they get stuck going one way, sometimes they get stuck the other way. Or they completely spas out.

My warranty from nintendo is long gone, but if someone can tell me how to fix it, if it requires replacing parts, then I could probably do it myself.

Looking online on google turned up nothing of use.

 

It looks like this might solve your problem:

This was taken from the 3DS manual, but this method is also listed in the 3DSXL and 2DS manuals, so it should work on any 3DS system you have. I hope this works!