I've seen a lot of people having similar problems on which the screen will start flickering if the system is not registering the face properly, but I've been kinda concerned about mine.
It seems like sometimes, the image that my left eye is supposed to see starts to flicker. If I close my left eye, everything looks fine, but if I close my right eye, I can see the flickering. If the system is calibrated fine, the it all works smoothly, but it's when it goes out of sync that the left eye messes up. I noticed this happening mostly when I had a light over my head because when I turned those lights off and left the lights across my room, the game was working perfectly. For the most part. I too have those random issues where it's difficult to get it just right sometimes.
Has this happened to anyone else? In that "one eye" will start to flicker?
This kinda reminds me of the Virtual Boy, where one eye could literally go bad.
But the 3DS doesn't operate like the virtual boy in that there are 2 LCD screens. With that system, bumping it or hitting it hard could cause it to unsynch, but as far as I know, the 3DS is just one LCD screen that produces the same images twice to produce the 3D effect.