What I know is that if you have a Factions character who was somehow ferried to LA without taking Chaos in Kryta (via Kamadan or teaming up with someone in Kaineng who did have the quest), they can no longer pick up said quest from Guardsman Chienpo (source -
http://wiki.guildwars.com/wiki/Chaos_in_Kryta). That said, it still does not explain why the character in question cannot pick up any primary quests in Prophecies as none of them have any prerequisites. Grafin does not know the means the character took to get to LA because it is a guild member who is having the issue. We had found out about it recently when the person arrived at Droknar's Forge and was looking to pick up Seeking the Seer from Captain Hugo Bronzebeard, who would not give the quest (which does not have any prerequisites).