http://www.gamesas.com/topic/1399783-dialogue-no-longer-works/
There is a bug with the current version of Skyrim, in which a mod's custom Dialogue in quests, Scenes, Story Manager Events, and SayOnce dialogue, are not working as they should. Workarounds have varied results, and testing has been done by many people. The conclusion so far is that the game itself does not initialise the Quest properties (dialogue etc) properly until a save is loaded with the mod in question active and enabled. The save file does not need to know the mod. The game just needs to load a save file twice for these properties to work. Even then, people are reporting things aren't working still.
The following were my test results, when it was thought to just be a dialogue issue:
==============================================
From my post further down the thread:
Ok so after further testing I have found the following for dialogue only "quests":
(My dialogue only quests are a single 1 line topic/response branch with a condition S - GetInFaction - HunterFaction == 1, and a single line with S - GetIsID - Elrindir == 1)
COC from main menu
No dialogue shows at all for hunters or Elrindir. No amount of waiting or fast travelling seems to solve this. SQV MyQuest shows the quest as running fine.
Load a save that has never seen the mod
No dialogue shows at all for hunters or Elrindir. No amount of waiting or fast travelling seems to solve this. SQV MyQuest shows the quest as running fine.
Load a save that has been saved with your mod loaded (I loaded an old save, and instantly saved it to make this new save)
All dialogue works perfectly!
(For testing) Load a clean save as above, then go to hunter (no dialogue shows). Save game right there, then load that save from the ESC menu.
All dialogue works perfectly fine!
Basically, your dialogue only shows if you load the game with your mod enabled, save it, then reload that save. So this is completely reproducible. I added the COC test results as I know some modders use that. I myself use it to test level design etc.
Something has definitely gone wrong with the latest patch, because any save loaded with a new ESP (my own for example) would instantly work fine with new dialogue quests. Now though, you need to save, then reload that save...
EDIT
Obviously this can cause problems because if you save with a mod loaded, that has an active quest with scripts, then those scripts will be saved into that save. Meaning any edits you make to it in the CK won't change for that save.
EDIT 2
A couple of people have reported this doesn't fix the issue, but more have said it does. Best to try it for yourselves. Until we get a fix from Beth

==============================================
It was initially thought to be a dialogue issue, but upon further testing there are deeper issues here affecting the entire Quest structure. At best it's all quess work as to the actual problem/cause, until we get official word on this. PM's have been sent to the Bethesda folk we have contact with. Fingers crossed this problem can be resolved soon.
Things to note from Sollar's testing:
2) The problem is not in the SAVE file, but in Skyrim itself. The "reloading a save" trick doesn't actually require saving the current game. The work-around can also be accomplished with the following:
a. Activate your mod
b. Load any save with the mod active
c. Load the "clean save" file (in this case, "clean save" = save file that has NEVER seen the mod, ever.)
Edit: The randomness of it works for some people and not others does NOT seem to be performance related.