Several things are confusing in this report.  You mention that it comes
up with a 29x39 dpi, however none of your log files show that dpi.
Second, your xorg.conf appears to be hardcoding the DisplaySize... why?
Third, your xdpyinfo.txt file shows 1280x1024 pixels (361x203
millimeters), which is  90x128 dots per inch, and that does not look
incorrect.

One other question, are you using GNOME or KDE?  On Jaunty's GNOME it
should already be forcing it to a fixed dpi, which gets around a lot of
the issues.

Beyond this, I've written up a guide on how to debug font size issues due to 
incorrect dpi.  Please review this and update this bug with the relevant 
information:
https://wiki.ubuntu.com/X/Troubleshooting/HugeFonts


** Changed in: xorg (Ubuntu)
       Status: Confirmed => Incomplete

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Incorrect autodetection of appropriate DPI
https://bugs.launchpad.net/bugs/394498
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