After the upgrade from 10.04 to 10.10 I noticed the Ubuntu theme was sometimes reverted to the default Gnome one, meaning fonts, icons, toolbars are all reset. I tried a clean reinstall but the same bug raised up again.
It seems to be a race condition appearing on higher hardware (combination of SSD + core i7). The internet provided me an ugly (yet working) workaround.
The file that I changed was /etc/xdg/autostart/gnome-settings-daemon.desktop. I changed the line:
Exec=/usr/lib/gnome-settings-daemon/gnome-settings-daemon
to this:
Exec=bash -c "sleep 2; /usr/lib/gnome-settings-daemon/gnome-settings-daemon"
to add a 2 second delay. And after rebooting, the theme is now properly applied.