Yesterday I was able to fix it and make it work with the multiple queues. I really cannot do without it.
It works pretty well now and along with those queues it was a refreshing addition. Now you can spend some time in Warsong (finally alive) and Arathi while waiting for a spot on Alterac. More action and less waiting time.
My mod makes you join automatically the battleground in the case you are atl+tabbed doing something else, there’s a customizable delay so that you can still have time in the case you are busy doing something else and prefer to leave the queue instead of joining right away.
The mod also works along with CTMod, so you need it to configure the options.