I see that you are editing in a floating window. Please edit your Photoshop Preferences and change your preference to open images in tabs. Then run the Layer Comps to Files script to see if it works then. There is a nasty bug in the windows version of Photoshop CS6 which causes Actions and Scripts that switch between document to fail. What seems to be happening is that an action or script step starts to execute a Photoshop command before the document switch completed. If the command requires an open document it fails. Adobe doesn't do a good job of system and regression testing these days. They started a few releases ago to release Beta versions instead thinking these would shake out the bugs. We are paying the price now for the last good release of Photoshop was CS3.