Caydiem responded in the Blizzard forums regarding the Alterac Valley queue system and issues with Alterac Valley in general.

Yes, a Blizzard Poster is responding after this long.

Understand that I approached the server folks earlier about this and they said that it was working fine. I wanted more in-depth information about it, however, and as such I continued pressing on.

The following is what I have for you.

You first noticed a change when the Warsong Gulch fix was introduced, and there's a reason for that. When that was patched, there were improvements made to the queue system. Previously, characters would remain in queue even if they logged out. As such, the requisite 30 people would be met on each side even if there were only 10 Horde players actually online, and the "Not enough players" countdown would begin. Thus more instances would start but not many of them would actually hold the right number of people.

You can read his whole reply and the thread here.