Where'd the Jockey go. Continuity??

Ok so saw it today. Yep, brilliant, BUT. Watched the Alien scene this morning before seeing it, so it stuck in my mind. When John Hurt and others go down to the planet in Alien, firstly, they see the big U shaped ship standing up, so it looks like a U (also makes you wonder what way up the big chair room is if its level inside) but ANYWAY. They go inside the room with the big chair, and see, sitting there, big alien crew member, the Space Jockey. Yep got his mask on and everything. But ok, he's sitting there, with a whole in his chest "looks like he exploded from the inside", so yeah, xenomorph. Ok so heres my question, at the end of Prometheus, the SJ goes after Shaw, gets fucked by the original facehugger, and dies there, in the Vickers medical bay. This, therefore, I have concluded, would mean that he would NOT be in the big space chair, where John Hurt and others find him. Anyone got any explanation for this? Again, love the film, but wasn't Prometheus supposed to answer exactly this kind of thing?