[DanCooper]

Check your settings for auto renaming. I do the exact same thing and works as should on latest alpha. When you scrape a show it will be given a unique ID.

Thanks, I think that's it. Never noticed the settings for DB update    

When I add new episodes to an existing show, they are not automatically renamed - I do have the settings for DB update enabled.
How do I ensure/check that a show has a unique ID? 
Is that in the .nfo file or the EMM DB?  

There is a new bug in the latest daily version: new episode files will be renamed but not moved into a season folder. I fixed it already and it should be included in komplex next build: Github

Unique ID is the TVDB, TMDB or IMDB ID of the tv show and it's saved in the DB of Ember (and inside the tv show NFO). You can check the NFO or in the context menu of a tv show: if the "Open on ... Site" is enabled, then this ID is available: