Same problem, fanfan.
My friends has same problem with project tree.
When I add folder with any project to left sidebar with project tree - many folders are empty.
I press many times: Project => Refresh Folder, but it's not help me is 50% times.
Yes, sometimes it's helps, but sometimes it doesn't.
I have problem with Window and Ubuntu.
Sublime it's great editor - but this bug makes me angry.