Well Sten, it was stated earlier in the episode that this specific nerve agent had to be inhaled to be effective (or Jack would have brought it back into the room with him, killing everyone). The air filtration system activated, and did you notice the delayed reaction of the security guard and the hobbit? At first they thought they were going to be okay, but then...bam! there was enough to kill them.
It took time, I guess, for the filtration system to filter out enough of the gas to make it safe...Chloe at one point said they'd reached the level where it was no longer affecting the seals, but that it was still too high to be safe...and that was when the two of them couldn't hold their breath anymore....