I just updated my x86_64 partition and my i386 partition (both FC6). When I rebooted x86_64 after updating i386, I got a message that it couldn't create the /var/lib/dbus/machine-id file. Sure enough, there was no /var/lib/dbus directory. I created it by hand and dbus was happier. I looked over in the i386 root partition, and it did have a /var/lib/dbus directory. Did the x86_64 dbus rpm leave that bit out or something?
