Space Jockey/'Alien' Connection: HELP

Matt N.
MemberOvomorphJune 05, 2012445 Views4 RepliesI saw the film last night and overall really enjoyed it. The only really bugging me is this:
In "Alien," the crew finds the SJ sitting in the pilot's seat with a hole in his chest indicating a chestburster exploded from inside him. In "Prometheus," we see the last Engineer take the SJ position to fly off to Earth, but then crash. Later, though, the Engineer attacks Shaw and is killed by the now grown squid in the escape ship.
My question: Why don't the events sync up? I expected that the SJ would have been infected by a face hugger, the xeno exploded from inside him and that's why the ship crashed, but that not what happened.
PLEASE HELP! This is driving me crazy.