Were the fleeing Engineers already infected? And if so why would they run TO the refrigerated chamber of Black Liquid, noting that this one chamber was more of a Temple (with the giant head) as opposed to the much more boring (and apparently un-refridgerated) cargo holds elsewhere in the movie? Was it that they felt the freezing temperature would stop the gestation of the Black Liquid in their systems? Or, were they fleeing to the refrigerated chamber because the door was the strongest to keep out the monsters chasing them?
I'm just speculating based on seeing the movie twice, but I think it was one or both of these:
engineers were running from something dangerous, perhaps an infected member of their own species who had gone homicidal (like Fifield does when he is infected)
some or all of them had been infected (as evidenced by the decapitated engineer, who appeared to be in the early stages of infection) and the chamber contained some sort of antidote
Finally, it could be:
- the decapitated engineer was the only member of the running group that had been infected, and that the others were running from him -- and used the door to kill him via decapitation
It seems to me that they created life, and not only on Earth. It could also be that they were running from one of their creatures, coming from another planet, and the black liquid is for trapping them. You never see what happens to an "engineer" if he/she is infected. If I were to produce a biological weapon and be so intelligent that I could plan life, I would probably make the biological weapon that protects me from my creatures harmless to myself. (And if I was so intelligent then I would not dissolve myself, but create a medium who can do the dirty work - so probably "engineers" are not the real engineers, but that is another topic.)