You know, I should mention, PaladinRider was having very similar problems with NPCs refusing to execute packages in a landmass mod he was creating, as detailed in http://www.gamesas.com/topic/1354960-npc-ai-packages-have-got-me-stumped/. I think he ultimately concluded it was the navmesh bug preventing the NPCs from moving. Or it was, at least in part. I recall that your project also involves creating a new land, so perhaps you're having the same problem? You could try doing basically the same quest/alias/packages but in vanilla cells and seeing if that worked, as something to compare with.
Anyway, I don't know if it will help, but here are a few screenshots of my quest/alias/package setup:
http://skyrim.nexusmods.com/imageshare/image.php?id=54946
http://skyrim.nexusmods.com/imageshare/image.php?id=54947
http://skyrim.nexusmods.com/imageshare/image.php?id=54948
I'm quite certain that I'm not doing everything in the Bethesda-approved fashion, but hey, I'm new at this, and it seems to be working, so I'll take what victories I can get.
All your stuff looks indentical to mine... Except you have a few other things on the alias in addition to packages. Gah. Also, the two alias's on my second quest refuse to fill. They are Unique Actor Alias's with absolutely no prior requirements of any kind or anything. I made them specifically for these two quests, yet they wont fill. I get this: http://cloud.steampowered.com/ugc/487752425900006332/2D75BC40EC1ACB1BD595DC65C4339012F76FA347/
Nobody is doing their packages.
And I don't think its navmesh issues. My mod is an esm, and I have bandits in several of my dungeons that function perfectly fine. I think it's something screwing up with these damned quests...
EDIT: So I changed all the people to Forced Ref's just to see what would happen; the Alias's in my second quest now fill properly, however they all still ignore their alias packages. Though, I used a loophole in my dialogue to trigger a Scene that's part of the second quest, and it went off without a hitch. My guard walked to a switch, activated it, said a dialogue line, waited a few seconds, then the scene ended and he defaulted back to his package. So the ONLY part that isn't working is the god dang alias packages.
I may just place packages directly on everyone to get around this. It will be messy, and just like Fallout, but at least I can move on...
DOUBLE EDIT: I just thought of something... I'm using the condition 'GetStage' on my packages. But I notice a huge amount of vanilla ones use 'GetStageDone'. Is GetStage broken or no longer used in the CK? If all my packages have false, or broken conditions, I imagine the game would ignore them...
Do either of you have functional packages that have quest stage related conditions? Which ones are you using?
Nevermind, an equal amount of their packages just use GetStage... Gaaah!