No, they got the wings retracted which is why it stopped, and also why it wouldn't pull in fully (if what I said about a force was true). The problem was that when the gate finally would close due to their built in timer, the puddle jumper would be cut into, one part would still make it to Atlantis, but the guys in the back would suddenly be in vacuum in space with the severed back part.
So they had to find a way to make it inch forward, now that it wasn't stuck. Hence the final part that I won't spoil here.