Tue Apr 05, 2016 8:05 pm by MiRai
If I'm correctly understanding your issue, then, as bob already stated, there was a change to the way that Battle.net functions which affects people with multiple accounts.
By default, ISBoxer virtualizes the config.wtf file for each of your characters, and the config file used to have a "LastServer" line which told the account which server to load into. However, that line no longer exists in the config.wtf file and the information seems to be stored on Blizzard's servers, which is why you are initially being pushed to the team/server you last logged into.
This can (sort of) be verified on the WoW login screen since there used to be a server name written between the "Credits" and "Quit" buttons where you enter your BNet e-mail and password, but that line of text indicating the last server has since disappeared with the recent update. That would likely indicate that this information is no longer stored locally.