Problem with modified files showing up in Git but not updating?

I've got some files/folders that just wont leave the Git staging area?

# On branch master
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#   (commit or discard the untracked or modified content in submodules)
#
#   modified:   JavaScript/Stand.ard.iz.er (modified content, untracked content)
#   modified:   Site (untracked content)
#   modified:   Template Archives/Template (modified content, untracked content)
#   modified:   Template Archives/Template_Git (modified content, untracked content)
#

I've tried everything to get these 'modified' files commited but with no luck?

I've tried...

git add .
git add *
git add -u
git add {actual full directory path}

...but none of it works.

Any ideas?

Thanks.