More on this:

There is a related issue which I think only happens on windows. After
I do a commit, all the files I committed would show up as being
modified. But in this case both magit and git-gui will be sync and
report mode change 644 to 755 and no content change. For some reason
windows changes the file permission. I didn't notice it at first as
the modes in dired didn't change. But inside a bash shell I saw that
the file modes had changed. But in the case I reported, git-git and
git are not in sync with magit and the file permissions haven't
changed.

On Aug 1, 7:28 pm, babusri <[email protected]> wrote:
> Using latest magit. I am using emacs 23.1.1 on winxp.
>
> I sometimes use git commands directly from emacs using 'compile' and I
> also use git-gui in addition to magit. I did a commit with git-gui and
> with this only one file is shown as modified in git-gui. This is
> correct. But magit shows that all the files are modified. That is, all
> the tracked files are shown under "Changes:" as 'Modified'. This
> doesn't change when 'g' (magit-refresh) is pressed. After pressing 'g'
> a few times, sometimes magit shows the correct output. But if I press
> F5 in git-gui and then press 'g' in magit, magic shows all the files
> as being modified.

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