There were a few problems when the battle.net login servers had issues. I didn't have ANY login issues with 3.2 I've been on battle.net login since the first day it went live.

But to the actual OP's question:

I use ISBoxer, which virtualizes the config.WTF file, which allows each wow to store it's own settings to it's own individual file, thus always opening with the correct account selected from the drop down. If you don't use ISBoxer, you should look into symlinking your installation so you can separate WTF folders for each toon.