Today while working on my local working directory under Git, I renamed a file from uppercase to lower case. (I am on Mac OS X Lion)
When I entered
git status it told me:
# On branch master nothing to commit (working directory clean)
After googling a little I found that the option ignorecase was set to true in the file .git/config
I changed it to false and the problem was solved. I do not know why it was on true if I am working on a Mac, and I have cloned from a Linux server. But it may help you.