The end of this post from Yoshi P explains it: http://forum.square-enix.com/ffxiv/threads/88643

In short, the log in queue is not for the server where you play. It is for the server that handles character log in. It makes sense that we'd be getting more of these queues these days because the number of worlds increased, but I don't recall seeing anything that said the number of lobby servers increased at the same time.