Hi, Julien,
1). As you said that the "For your information, I'm using a 640x480 resolution 
on a 5 inches touch screen panel." What is mean about it? and I saw your 
xorg.conf file, I suggest try to amend the Section "Screen", see below:

Section "Screen"
        Identifier "Screen0"
        Device     "Card0"
        Monitor    "Monitor0"
        SubSection "Display"
                Viewport   0 0
                Depth     1
        EndSubSection
        SubSection "Display"
                Viewport   0 0
                Depth     4
        EndSubSection
        SubSection "Display"
                Viewport   0 0
                Depth     8
        EndSubSection
        SubSection "Display"
                Viewport   0 0
                Depth     15
        EndSubSection
        SubSection "Display"
                Viewport   0 0
                Depth     16
        EndSubSection
        SubSection "Display"
                Viewport   0 0
                Depth     24
        EndSubSection
EndSection

BTW: you can reference my attachment file about the xorg.conf. Use this
conf reproduce the phenomenon.

2). Now my xf86-video-geode version is 2.11.8, XServer version is 1.7.1,
I can't reproduce your phenomenon. If you try to use the latest version,
please tell me how to reproduce, I'll follow it.

Thanks,
Hunk Cui

** Attachment added: "My xorg.conf file"
   http://launchpadlibrarian.net/49110494/xorg.conf

-- 
Black margin on the left of the screen with geode driver
https://bugs.launchpad.net/bugs/377931
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