I'm not too sure what is going on here, but sometimes a particular file in my repository will change the case of it's name. e.g.,:
before: File.h
after: file.h
I don't really care why this is happening, but this causes git to think it is a new file, and then I have to go and change the file name back. Can you just make git ignore case changes?
[edit] I suspect it is Visual Studio doing something weird with that particular file, because it seems to happen most often when I open and save it after changes. I don't have any way to fix bugs in VS however, but git should be a bit more capable I hope.