@Seliph the clock overlay does that because it refreshes the whole screen (top and bottom) when it updates it. The blue reduction function is trying to change the screen as well so they're fighting each other. Not sure if they were using a different way to reduce the blue light in it before (change the color in memory instead of constant updates?) if it didn't happen. I don't see it happening in 2.6 w/o an overlay, but I may also be blind.
@Distrance just turn off Windows Defender before you try to download it, copy it to your 3DS, then turn it back on. You can even make sure if you're paranoid @
VirusTotal.