Blizzard does extensive scans of battle.net looking for duped items, and when it finds them, they poof. You can have it as the only item on the only character on the only account that you made with a cd key, and it would still vanish. Two people joining the game with identical runes just speeds up the "poof process".
really, how come all those dupe runes still exist then?
Hell if I know. Do I look like a blizzard tech support agent? I'm just stating what blizzard told me in a phone call I made to them after a few more of my runes and my friend's CTA poofed.
Besides, new duped runes are showing up all the time. Get rid of the old ones and new ones will just spout up.