So I probably don't need to tell everyone that since Patch 1.6 there have been some problems with creating quests that contain dialogue. We all refer to it as the "dialogue bug" and it's been a pretty big thorn in everyone's sides if you're making quest mods.
The gist of the problem is this: You have quests with dialogue. These quests are marked as "start game enabled". Your quests start, but the dialogue is not properly initialized. Your dialogue therefore fails, any attached script fragments MAY fail, and your scenes don't play. We've been waiting for a fix for it for some time now. That wait is over.
Recently, I was approached in private by one of the Bethesda developers (if they wish to identify themselves, they can, I won't out them) to test a potential workaround for this issue. After some initial testing, and seeing that it appeared to work, I asked them to contact Alexander J. Velicky, the author of the Falskaar mod, for another opinion since I knew he has a ton of dialogue related issues as a result of all this. He too has since confirmed the workaround fixes the problem. Fortunately, it's actually fairly simple to do.
The process, using Steam:
1. Go to Steam. Switch to the tools view.
2. Find the Creation Kit, open its properties.
3. Click "set launch options"
4. Enter a command like this: -GenerateSEQ:pluginname.esp (Where pluginname.esp is your mod file)
5. Save the changes.
6. Launch the CK and DO NOT disturb it while it processes.
7. Once it closes, remove the launch options you entered so you can use the CK normally again.
8. Move the file to your Data\SEQ folder.
You can also do this from the Windows command line:
1. Open CMD.
2. Navigate your way to where Skyrim is installed. (By default: C:\Program Files\Steam\steamapps\common\skyrim)
3. Type in the following command: creationkit.exe -GenerateSEQ:pluginname.esp (Where pluginname.esp is your mod file)
4. The CK will launch and perform some processing.
5. Move the file to your Data\SEQ folder.
Note that the command line process may only work once. I've never been able to get it to work again since the first try. So I had to switch to the Steam method, which Alexander suggested.
The SEQ file will need to be regenerated any time you add a new start-enabled quest to your mod, delete one from the mod, or toggle the "start game enabled" flag on a quest in your mod. So it's important to remember this.
When I tested this, the command line option only worked once and has failed to ever work again. The Steam method works without fail each time, but it's a pain.
Good news is, once the developers cleared Alexander and I to share this knowledge, I contacted Zilav (TES5Edit) and he'll be including support to generate this file through TES5Edit as well.
The file itself is nothing more than a series of form IDs for each quest in your mod that's been flagged as start-enabled. It's encoded though, so you can't just type it out by hand.
TES5Edit will be the easiest method for generating this file since it will place it in the proper folder for you, rather than the CK simply dropping it in the same place as creationkit.exe.
Distribute the generated .SEQ file with your mod in the usual fashion.
At this time, we have not been told whether or not this will be included as an official menu option within the CK. So for now just proceed as though it won't be added to the UI.
Modders should be the one to generate this for distribution, but in a pinch, users can also follow the steps until modders can get around to generating it.