Apart from SkyRe I dont have any mods that would mess with anything in the game, all of my other mods are extra armors, weapons and other non-replacer content.
I tried restarting the game, looking for an NPC that will give me a Misc quest, but once I tried to speak to them, the dialogue option that starts the quest wasn't there.
Has anyone encountered this problem before?
Edit:
I have found a way to fix this. All you have to do is somehow force a misc quest to appear, it will bring back the Misc quest list with all of the misc quests you had before it went away.
To do this you can use the console or simply adopting the beggar kid at Whiterun will work too.