I figured it was something like that, as you are very consistent in that regard. I've done a quick trace of the methods (because I'm curious too and giving you the most information will probably make the bug, if it exists, easier to fix).
I think the path getting passed to get_files(), well initially the "fuzzy_file_nav" command, is "C:". os.listdir() is then called on this, which is where things don't happen like one would expect. When you enter "C:\" as the path, the "start" variable already contains the slash ("C:\")
Well with that, I don't think there is any more information I can think of off the top of my head to help reproduce the issue. I'll check back tomorrow though, so let me know if there's anything I can clarify.