It is indeed possible that screenshot tools which are not aware of OpenGL canvases may fail trying to capture an empty desktop plane.
Use the built-in feature instead: There is a command "/screenshot" with options: "/screenshot lossless" will save a PNG instead of a (rather low quality) JPEG; and "/screenshot nogui" will capture the 3D world only, without the GUI windows on top of it. Both can be combined. You can bind a shortcut to it.
The resulting files are then in %APPDATA%\PlaneShift\screenshots (in your user account's application data area, possibly a hidden folder, so enter this location into your Explorer's address line).
