Repo corrupted somehow?

["Andrew Arnott" <andrewarnott@gmail.com>]

I was just git commit'ing, and then I was doing a git rebase to squash
several commits into one when the rebase failed.  I then did a
git checkout -f master
git reset --hard
but no matter what I do, git thinks that several files have changed.
The diff shows all the lines in these several files removed and then
added, yet without any changes made to them.  git reset --hard doesn't
revert the change. When I jump around history with git checkout these
files remain in their "changed" state.  I even tried "git clone" to
create a whole new repo, but one of these several files STILL
registered as changed before I made any changes.

Any idea what's wrong and how to recover?

Observe the below command buffer: (I can upload my repo so you can
clone it and perhaps repro it if you want).

Andrew@LACKY /c/git/dotnetoauth
$ git status
# On branch master
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#
#       modified:   tools/Documentation.targets
#       modified:   tools/DotNetOpenAuth.Common.Settings.targets
#       modified:   tools/DotNetOpenAuth.Versioning.targets
#       modified:
tools/Sandcastle/Presentation/vs2005/Content/reference_content.xml
#       modified:   tools/libcheck.ps1
#       modified:   tools/sandcastle.targets
#
no changes added to commit (use "git add" and/or "git commit -a")

Andrew@LACKY /c/git/dotnetoauth
$ git reset --hard
HEAD is now at 13d37b8 Patching up the bad merges in the phases.

Andrew@LACKY /c/git/dotnetoauth
$ git status
# On branch master
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#
#       modified:   tools/Documentation.targets
#       modified:   tools/DotNetOpenAuth.Common.Settings.targets
#       modified:   tools/DotNetOpenAuth.Versioning.targets
#       modified:
tools/Sandcastle/Presentation/vs2005/Content/reference_content.xml
#       modified:   tools/libcheck.ps1
#       modified:   tools/sandcastle.targets
#
no changes added to commit (use "git add" and/or "git commit -a")