I don't think anyone has ever came upon this problem with the CFW, I think if it isn't the other DS's problem, then your 3DS's download play is broken for some reason. I personally have no idea how this could happen, or what has completely happened, but this is very odd. Best of luck!
Caller -"Everytime I start a Pc game on my S24, playing on a external monitor, someone calls or texts me, n it kicks me out of the game." Customer Support - Click (hangs up)
I found it funny cause many many years ago, had a roommate in college that did this same dumbass branding of the school logo, but it didn't look anything like it after it healed. Just looked like a birthmark.