This is a wild guess but it may be because the first objective always shows up (which is to kill the npc group) The other ones wait until the pop up dialogue is complete before being "in progress"
What I did in "The Great Escape" is have an invisible wall between the player adn the npcs. Then have the first pop up dialogue be a Map pop up dialogue and hook the visible->invisible trigger for the invisible wall to be component complete on that pop up dialogue.
This problem even exists in Cryptic maps. The last mission in the Romulan chain, where you fight Hakeev... When the mission starts, everyone starts fighting and Obisek's pop up dialogue will be interrupted by combat almost immediatelity.