git has modified files after clean checkout

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here's what I did

rm -r portage
git clone git@xxxxxxxxxx:xenoterracide/portage.git
cd portage
git checkout origin/regen2 -b regen2
git status

# On branch regen2
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#
#       modified:
x11-themes/metacity-themes/files/metacity-themes-1.0-gentoo.diff
#       modified:
x11-themes/metacity-themes/files/metacity-themes-1.2-gentoo.diff
#
no changes added to commit (use "git add" and/or "git commit -a")

why are there files claiming to be modified? this is a clean clone.
I've had this before I usually end up doing a git reset --hard HEAD,
but I'm thinking it's a bug, since I've seen it vary on the same clone
and sometimes even disappear.

git version 1.6.0.6
-- 
Caleb Cushing

http://xenoterracide.blogspot.com
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