I switched to the ST3 beta (build 3047) a few days ago and today the folders in most of projects are shown as empty.
The first problem I noticed was that when I started ST3 this morning it reopened two projects (as I wanted it to). One was fine, but the other had visual bands of corrupted pixels mixed in with the list of files in the sidebar. For that one I tried toggling show/hide but every time I hid a folder of files when I showed it again it was empty. Removing the folders and re-adding them did not help: still empty. Most other projects I have opened up since then just have empty folders (and none have shown the corruption). I'm on a Mac running 10.8.5 with the supplemental update.
I tried Refresh Sidebar and that had no effect.
I also tried disabling Sidebar Enhancements and quitting and restarting ST3 but that did not help. (I then then re-enabled Sidebar Enhancements and again quit and restarted ST3, but the problem is still there).
I also had a situation where ST3 was using all available CPU power for many minutes when I added a folder to a project. I presume it was reindexing something, but who knows. At the end of all that the folders were still shown as empty.
I tried switching back to ST2 and it seems OK, so I'll just run that way for now. But if anyone has a suggestion how to get my folders back, I'll give it a try.