Did you complete the story quest (kill Bloodwing) or not? There's apparently a known bug whereby if you complete that mission without collecting ten slag samples, you can't restart in the level at the NSA.
Am I doing it wrong?
I had a go at the Docter's Orders/Jimmy Jenkins exploit last night and while on my first go I managed to get 3 mini-loaders from 4 boxes (no decent loot though), I was under the impression that you could use the Creature Slaughter Dome (Natural Selection Annex?) as your save-quit-reload point, to save another slog through the whole level? I returned to the Natural Selection Annex, quit and reloaded, but it returned me back to the beginning....
Lie with passion and be forever damned...