Start conky only after the root window loads
Every time I logged in, conky would start up before nautilus loaded the desktop. This caused conky to load as a floating window that stayed on top of all other windows. I have finally gotten around to fixing this problem.
~~Here~~ (gone, email if found) is a simple python script that waits for nautilus to load the desktop before starting conky.
This script is probably very inefficient but it gets the job done.