Find the solution. Simply unsubscribe and subscribe one civ in game, and all the civs will be synced. Before i subscribed off game and all were present when i started a new game.

Well, i dont know why, but it now works as i mentioned.

Hope this help.

I've just had the same problem and have been working on fixing it all day. All the normal methods (reinstalling, purging etc) didn't work but have stumbled on this solution;
In steam right click on game, properties, go to betas and opt in to the 2.8 version of the game. Allow it to update and then run the game. In my case all the downloaded workshop content magically appeared.
Then just quit out of the game, go back to steam and opt out of betas and again allow it to update. Then you should find you're up to date with version 3 and the workshop content is now working again.
I should point out that I have not (yet) got the intrigue DLC and I'm guessing that maybe this is the cause of the hiccup.
Hope this helps.