Hi, sorry to dig up an older post.
I'm having this same problem after upgrading from 0.6.0 to 0.6.1. The categories are still there if I view profiles and see the account's recent posts or if I click on the "Forum" link, but when I first load up the page or use the $home link at the top-left nav bar, the categories don't show.
The upgrade was a bit bumpy with 3 conflicts that were resolved with a "git reset --hard $hash" and an out of date schema with "./nodebb upgrade".
I started it in ./nodebb dev mode and went to the $base_url/debug/cid/1 in my browser and see the json attributes of the category, but don't know where to go from here.