A change of behavior in XEmacs across a reboot like this that you
don't expect almost certainly means you've upgraded something,
possibly the X font server, possibly something in GNOME.
For the default fonts, XEmacs indeed pays no attention to system DPI
settings, and shouldn't need to, because it specifies the font sizes
in pixels, and then accepts what the system gives it. It then
computes line heights and width based on character metrics which it
also queries the system to get.
For each version of XEmacs, what is the output of
xemacs -vanilla -batch -eval '(prin1 (face-font (quote default)))'
Maybe you have some X resources set that are specified in pixels.
What does "xrdb query | grep -i font" tell you?
What does xdpyinfo tell you about your screen metrics? Do they make
sense? I would not be surprised if the metrics specified for your
monitor are way smaller than actual.
Please also send the Installation file for each version of XEmacs. If
you can't find that, cut and paste the output of
M-x describe-installation RET (which is exactly the same thing), for
each version of XEmacs.
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