I've been modding for a while now and I've made several quests for my mod. A few months ago I suddenly had problems with getting quests to run, apparently caused by the quest aliases failing to fill. At first I thought I was missing some important step somewhere, but after making another quest with just one alias I didn't have any problems.

The mod I'm working on has multiple masters; Skyrim, Update, Dawnguard. We also have a .esm with our worldspace but I work inside a separate .esp so we can merge it with version control. I do not reuse npc's for the quests as I thought one of the reasons for not filling was conflicts with reserved references. I create new SEQ files every time I made changes to the files. Also of note: a quick testing plugin I wrote seems to have no problems with aliases, but I mostly used Story Manager Events to trigger the quests when entering the desired cell. Using the SM still didn't fix it in my mod, though.

I create a new game every time I test the mod, I save this game and restart skyrim. I have no other mods running besides the necessary masters and my own .esp. When checking ingame the quests are all running, but some of them fail to fill the aliases.

This is one of the quest setups that went wrong:

Quest with name, Side quest category, priority 60, Start game Enabled (Run Once off)

Quest Stages of 1 (Start Up), 5, 10, 11, 20, 200, 250. Stage 1, 5, 10, 20, 200, 250 have scripts to handle objectives

Quest Objectives for 1, 10, 20 with alias targets

Quest Aliases:

Mage, Unique Alias, Essential, has a forcegreet package

Located in Kynesgrove Inn

Sergeant, Unique Alias, Essential, has a forcegreet package

Located in custom worldspace

I can also post my quest dialogue setup but I'm 100% certain the problem doesn't lie there.

The latest release of our mod is already uploaded on Nexus, but it's around 500mb. The plugin which I have problems with isn't uploaded there but if needed that can be arranged.

Link to the mod: http://www.nexusmods.com/skyrim/mods/18795