For anyone having a similar problem than mine, I have found a solution and I figured I’d post it here for the benefit of the community. Here’s a little background.
I had a list of movies onganized as such:
All of the movie files and corresponding metadata resides at the root of each category. It’'s actually pretty neat as you can browse through the cover for each movie and get synopsis info, genre, actors directors etc…
I have always organized my files so that the folders with an underscore preceding the name would appear on top when browsing with explorer (old habit). The problem I had was that for some reason the _archive folder and its subfolders disappeared after each compile session (after reboot or cold start).
Well to my dismay, can you believe that by removing the underscore caracter, the hub immediately started compiling the media library and my archive folder (without the underscore) is now appearing with all its subfolders and content.
The morale of this tale is that the hub does not like underscores.
I hope that this will help someone.