Some themes are designed to be off-center, configured to appear at either edge of your screen. However, if you're expecting a theme that was designed to be at the center, and it appears out of alignment, have a look at the configuration and check for the value of alignment. Edit it to say 'middle_middle', and you should be set!
If you're still having problems, you may have changed your display resolution mid-session or are using your operating system in a virtual machine designed to scale the resolution as you resize the window. In this case, just restart Conky or the operating system, and this should fix itself.