I always work with the latest dev builds (the most stable dev builds I've ever seen, by the way ) and have the same problem.
I run Sublime 2 under Windows 7 (32bit and 64bit) and work with files on a samba share.
Files and folders only work down to the 5th level. Starting from the 6th level files and folders only appear when I click on Project > refresh folders. The following scan reveals the 6th level of all already opened 5th level folders. To see the 7th level, I have to use refresh folders again and so on...
Is this a wanted behavior to prevent performance issues? Would it then be possible to rescan >= 5th level folders automatically when opened?