Maybe u din solder the pogo pins to enough pads to give it strength or maybe ur pogo pins aren't long enough or ur wire got trapped by the shell as u closed it. U could do like n1ghty did, with rubber pads to help distribute tension on the pogopins if they're not long enough. Or even just add solder to the pogopins on the underside of the pcb too, that way they won't move.
I suspect ur pogo pin lifted cause when u closed the shell ur cuts on the pcb weren't big enough or not placed correctly and one of the protuberances of the shell pushed the pcb down lifting the pin and taking out the wire...
Mine didn't lift off the pcb cause my pogopins aren't strong enough to lift the copper from the pcb and, the 3ds shell itself presses them down, not the pcb.
I had mine setup as close to yours and n1ghtys as possible. I never had any rubber padding did however use white electrical tape. Unfortunately I got my proto board at RadioShack (nuff said) and I believe that the pogo pins are actually too long, or the cuts on the sides of the boards weren't the proper size. (case wouldn't close without bulging) I will let you be the judge http://www.amazon.com/Amico-Spherical-Radius-Spring-Loaded/dp/B008LTKMG4/ref=sr_1_1?ie=UTF8&qid=1393097542&sr=8-1&keywords=uxcell test pin spherical
Still if there is someone with better skills than I, I would be happy to commission someone to make one of these for me. In which case PM me.











