From "Stargate: Atlantis: Thirty Eight Minutes (#1.3)"
Dr. Peter Grodin
The Stargate transmits matter into discrete units... the front half of the ship cannot rematerialize till the whole ship is crossed into the event horizon. The Stargate is essentially waiting for the continuous component, that's meaning the Jumper and everything inside to enter completely before it can transport them...
Dr. Elizabeth Weir
[Beckett stares then lookes at Weir
] He says the Gate only sends things through in one piece.