Actually the Op isn't wrong. If you miss the commence timer it does NOT re-queue you, it boots you out and you have to rejoin and start over.

This happened to me the other day not because I was afk, but because I was soloing fates while waiting and got bored failing to do enough DPS as a healer, so I switch to Bard temporarily. The commence timer popped up, but I had to switch back to Scholar in order to join the instance; however at this stage I was fighting Svara. I ran like hell ut of the svara fight - but picked up an add on the way.

By the time i shook the add and switched back to scholar the commence window had closed, and to my surprise it didn't re-queue me i had to start over from the back of the queue.