I found the problem!

There's two reasons why this problem happens :
#1 : The /etc/qt3 folder has very low permissions which refuses anyone
else than root to access or list the files

In Gutsy : drwxr-----  2 root root
In Feisty : drwxr-xr-x  2 root root

#2 : The config file /etc/qt3/qtrc doesn't exist.

It isn't created during the installation process of the libqt3-mt
package. for a unknown reason, the /etc entry has been removed from the
debian/libqt3-mt.install file in the source package. Re-building the
source package after adding /etc gives a binary .deb which fix the
problem.

I attached a Debdiff which fixes this problem.

** Attachment added: "debdiff.diff"
   http://launchpadlibrarian.net/9891256/debdiff.diff

-- 
7.10: Qt3 ~/.qt owner root and missing qtrc result result in ugly appearance
https://bugs.launchpad.net/bugs/145709
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