I am seeing the same behavior and my observation matches user woeye’s posted earlier in the thread (viewtopic.php?f=3&t=7142#p33432).
It appears that Sublime Text proceeds in alphabetical order, finds the inode of the symlinked directory, then later skips the directory when it finds the same inode (even though that’s the “real” directory path, not the symlinked path).
In the example console output below, the “real” paths are:
/Users/me/dev/someapp/shared/spec
/Users/me/dev/someapp/shared/attachments
which are symlinked to from:
/Users/me/dev/someapp/my-first-app/spec
/Users/me/dev/someapp/my-first-app/attachments
and
/Users/me/dev/someapp/my-second-app/spec
/Users/me/dev/someapp/my-second-app/attachments
startup time: 0.93826 (package setup was not run)
scan: /Users/me/dev/someapp/shared/attachments has been seen before, skipping (using inode) previous path: /Users/me/dev/someapp/my-first-app/attachments inode: 3867976
scan: /Users/me/dev/someapp/shared/spec has been seen before, skipping (using inode) previous path: /Users/me/dev/someapp/my-first-app/spec inode: 543476
scan: /Users/me/dev/someapp/my-second-app/attachments has been seen before, skipping (using inode) previous path: /Users/me/dev/someapp/my-first-app/attachments inode: 3867976
scan: /Users/me/dev/someapp/my-second-app/spec has been seen before, skipping (using inode) previous path: /Users/me/dev/someapp/my-first-app/spec inode: 543476
scan: /Users/me/dev/someapp/shared/attachments has been seen before, skipping (using inode) previous path: /Users/me/dev/someapp/my-first-app/attachments inode: 3867976
scan: /Users/me/dev/someapp/shared/spec has been seen before, skipping (using inode) previous path: /Users/me/dev/someapp/my-first-app/spec inode: 543476
scan: /Users/me/dev/someapp/my-second-app/attachments has been seen before, skipping (using inode) previous path: /Users/me/dev/someapp/my-first-app/attachments inode: 3867976
scan: /Users/me/dev/someapp/my-second-app/spec has been seen before, skipping (using inode) previous path: /Users/me/dev/someapp/my-first-app/spec inode: 543476
I am not using Samba or any other network shares. This is occurring on my local drive on OS X 10.7.4. Seems like a bug to me.