After git reset --hard, git status gives me files within the Changes not staged for commit: section.

I've also tried git reset ., git checkout -- . and git checkout-index -f -a, to no avail.

So, how can I get rid of those unstaged changes?

This seems to hit only Visual Studio project files. Weird. See this paste: http://pastebin.com/eFZwPn9Z. What is special with those files, is that in .gitattributes I have:

*.sln        eol=crlf
*.vcproj     eol=crlf
*.vcxproj*   eol=crlf

Also, autocrlf is set to false in my global .gitconfig. Could that be somehow relevant?

I had the same problem and it was related to the .gitattributes file. However the file type that caused the problem was not specified in the .gitattributes.

I was able to solve the issue by simply running

git rm .gitattributes
git add -A
git reset --hard