Is it outside the workspace or outside the screen? With my own theme I have a bar at the top and bottom and the workspace defined as the area between them but sometimes non-maximised applications will be positioned under the top-bar but not off the screen. It's as though Windows doesn't respect the defined workspace area and assumes it has the full screen to use.

Try using a different desktop module to see if it makes a difference.

As a work around you will find that if you create a bang to toggle the size of the workspace between full-screen and not-full-screen (like Simplicity has) and execute the bang twice (say, using a hotkey) it will automatically move applications into the correct non-full-sreen workspace area. Hope that makes sense.