My way is revert all files after to close all files:
View/Show Console and enter command:
len([v.run_command("revert") for v in window.views()])
Or Save after Close all files:
len([v.run_command("save") for v in window.views()])
Then go to File/Close All Files
I tested on Mac OS and Sublime Text 2. You can try other version and OS.
Hope help you to close all files.