Audio problem: During the Tea Party scene, the Mad Hatter and March Hare ask Alice to tell her story. After the Mad Hatter says "And when you come to the end, stop!" audio follows of the voice director saying "great," leftover from the original recording. (00:45:40)
Audio problem: When the box of cakes appears, Alice takes one, and says "Goodness know what.", and then she puts the cake in her mouth, and is visibly not moving her mouth, however we still hear her say ".this will do."
Audio problem: After the flowers pour a load of water on Alice and she slides down, she says "they could learn some manners" but her mouth is not in sync.
Chosen answer: There is no real answer. It is intended to be left unknown. See http://www.straightdope.com/classics/a5_266.html for The Straight Dope's answer.
Guy