That's the first time I hear of this. I was thinking about setting up retroarch on my IPS console, so that's something to keep in mind, I guess. If this happens with F-Zero on Virtual Console it might happen with retroarch as well...
I never understood why people praised the IPS panels so much, by the way.
You get better looking blacks and the 3D effect has less ghosting (or maybe I just miscalibrated the 3D effect on my TN console), but there's a scanline like effect on the screen which depending on the game really gets on my nerves...
The screen is also much darker, even on the highest brightness setting.
And the console is quite a bit heavier which makes it less comfortable to hold and the battery doesn't last as long.
Maybe I'm in the minority here, but I prefer my 2nd New 3DS XL console with TN screens.
Edit:
Yes, I was one of the fools who hunted for an IPS console, only to be disappointed with the things I mentioned above when I got one...