From mboxrd@z Thu Jan  1 00:00:00 1970
From: "Alex Riesen" <raa.lkml@gmail.com>
Subject: Re: Gitk/Cygwin bug: phony local changes
Date: Tue, 28 Oct 2008 16:27:36 +0100
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References: <83bpx62hbn.fsf@kalahari.s2.org> <837i7s3ga4.fsf@kalahari.s2.org>
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To: "Hannu Koivisto" <azure@iki.fi>
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2008/10/28 Hannu Koivisto <azure@iki.fi>:

> I used bisect to find which commit introduced this bug and the
> result is:
>
> 7faee6b8de836904227ee98dc3d2c4c75b0ef3a1 is first bad commit
> commit 7faee6b8de836904227ee98dc3d2c4c75b0ef3a1
> Author: Mark Levedahl <mlevedahl@gmail.com>
> Date:   Mon Oct 13 00:33:31 2008 -0400
>
>    compat/cygwin.c - Use cygwin's stat if core.filemode == true
>

Could you try the patch from Junio's "Re: [PATCH] Only update the
cygwin-related configuration during state auto-setup" mail and see
if it changes anything?