Since the other thread got locked I guess I'll make a new one.
We experience a similar issue. We're ranked #2 on three boss kills, bosses nobody else on our server have killed (on either difficulty) and we've been ranked #2 on them for at least a few weeks by now. The guild has been refreshed several times since then, so it's not only "give it some time" anymore.
MCO on Shadowsong-EU:http://www.guildox.com/wow/guild/eu/Shadowsong/MCO
Bosses in question is Norushen, Galakras and Iron Juggernaut.
It seems to only be an issue at the guild view, because if you open up the individual achievements, we're ranked #1 (and alone):