I've noticed alot of people have been having problems running conky at startup in *buntu 12.04. I installed a newer version than is in the repos and everything just works now. (at least for me!)
Download the following two .debs and run sudo dpkg -i on them, and you should be good to go.
https://launchpad.net/ubuntu/+source/conky/1.9.0-2/ will give you the binaries you need.