I worked on this game twice, once back in 2008, and again right now. Previously, I did Agent Solo - Perfect Agent Solo - Dark Agent Solo....
I found a coop partner for DA, but when I hosted a lobby, only Perfect Agent was available to me for some reason. He had DA unlocked in coop, I joined his game and completed 1 DA level, and the achievement didn't unlock.
Sheltons method is best and required minimum playthroughs, Agent Solo - Perfect Agent Coop - DA Coop.
I think the way the game works is in order to get credit for DA Coop, you both need to run through coop PA, besides this method unlocks solo DA anyways..