i too had a similar problem after installing zotero on my macbook air. I was able to see all the collection of articles of all the in the middle pane, but the folders in the first column below my library was empty. After reading all your suggestions and trying it out nothing worked. Then i clicked on add new collection( the first yellow folder ikon next to the my library ikon) and added a new collection with a new name. immediately all the missing folders of my library appeared like magic. Thank you.