I start mine from a small script in my home directory. The script is added to gnome-session-properties and is called when I log into the desktop.
Debian 7 / Gnome Shell
Here's the script ...
PHP Code:
#!/bin/bash
# ck.sh
# Start conky script
# Glenn A. Johnson
# Started May 7, 2013
# Last edited May 7, 2013
# Written specifically for the Phenom box running Debian 7
sleep 5
conky -c /etc/conky/conky.conf &
sleep 5
conky -c /etc/conky/conky_black.conf &
It actually calls 2 conkys.
In gnome-session-properties for startup application preferences/startup programs I created new then I've added a name (Conky), command (sh .ck.sh) and description, (desktop eye candy).
Are you sure it's not already running? It seems that a lot has changed regarding conky with the advent of Gnome 3. Mostly display related.