Title

Alice's flashback is home to the title explanation. "Lately, [Jenna] had been afraid to fall asleep. Instead of a nap, Jenna called it the Leaving Time. She was certain that if she closed her eyes, I would not be here again when she opened them." 

So first, that is Jenna's little bit of psychic ability, like Serenity talks about. She knows her mother will vanish. 

Also, I think maybe the book is called leaving time not just because Alice vanished, but because Jenna is still haunted by the idea that if she doesn't do everything to find her mother, she will lose her forever. (At least at the beginning of the book)