This happens to me as well.
If I add files or folders to the project directory from the command line (say from git pull, or touch file.txt) the sidebar in Sublime Text 2 does not refresh with the new files.
This worked in the previous version just fine, but since upgrading to the new build (2181), the one with the fancy new icon, it has stopped working.
I'm running OS X Lion 10.7.3
Is there anyway to downgrade the version I'm using because in this current state I can not work efficiently, I'm finding myself going back to old habits and using the bloated and slow Eclipse IDE...
It's a shame because I really love Sublime Text 2, I bought a license even though it seemed to let me work without one, I was voting with my wallet that this is an App I want to support.
Many thanks for any help people can provide, and let me know if there's any more info I can provide to help nail down the issue to a specific component.