I've upgraded to Ubuntu 9.10 recently, and I can't get it to load my ~/.xinitrc when I log into Gnome.
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Do you log in using GDM or any other graphical login manager? They usually ignore .xinitrc and read .xsession instead.
You could symlink .xinitrc to .xsession or the other way around to keep them synched:
ln -s .xinitrc .xsession

Mikael S
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