I have: http://windows.github.com/
My current project has around 20k files, around 150MB (and not speaking about how slow it is and I cannot do a thing now) it doesn\'t
So guys this is the full steps I had to take in order to fix the problem...
1) Using Process Explorer (you can download it form here http://technet.microsoft.com/en-us/sysinternals/bb896653.aspx) I searched for any process referencing ".git\index" and then I killed it.
2)Then using Git Shell (Windows Power Shell) I went into the repository which was giving me such difficulty and then furthermore went into its .git folder. (cd .\your_respository_name\.git). I then removed the index.lock file in that directory (rm -r index.lock).
3)Then from within that same directory I ran git reset HEAD.
4)Then I manually committed each file using the "git add [file_name]" comand. (You can check that they were added successfully if when you run git status, the files are green.
5)Next run git commit if your files are added correctly.
6)Finally go back to github for windows and sync everything up and it should hopefully work and resolve the problem.