For a specific project i have, I had the folder previously named like so: MyExampleApp. I removed it at one point and re-cloned the source, and it is now: myexampleapp. However, ST2 was still showing the first version. More importantly, anytime i would create files or folders, the pane on the left would not automatically update. For any other app or site I'd work on, it was fine. Just this specific folder. I tried deleting the Session file, but that did not fix it. Deleting the session however did fix the name of the project when i have it open to be lowercase.
Note when i mean project, it is not a sublime text project. I simply open the top level directory.