I had a very weird bug last night that I can't explain. I had an error pop up that basically said the colour scheme that I was using was empty and couldn't be read (sorry, I didn't get a copy of the actual error). At the time I was using my own custom scheme, which thankfully I had a backup of elsewhere. However, when I switched to the default Twilight scheme, it did the exact same thing.
Somehow Sublime was deleting the contents of the scheme files. The files themselves remained, but they were empty and 0k in size. I tried quitting and restarting the app, but the problem persisted. When I would try to copy my scheme back to the folder and then change to that scheme it would seem to load but it would empty itself and the error would pop on the first file that would load. The scheme would turn to a white background with black text. I tried rebooting, copying the scheme, deleting the scheme cache, and finally I reinstalled the app several times. Eventually the problem inexplicably went away. However, uninstalling and reinstalling the app does not replace the Twilight theme that is now missing since I deleted it and its cache.
I'm sorry this is all a bit vague. I really should have got a copy of the error that was popping.