Run the pssetup.exe application (it's located in the directory where you installed PlaneShift, usually C:\Program Files\PlaneShift Crystal Blue) - and change the resolution of the game to be lower than that of your monitor. So if you're running your screen at 1024x768, run the game at 800x600. This will allow you to reposition the game window and center it, and then you can change the resolution again.
If you're not sure what your current screensize is, you can right-click anywhere on your desktop, hit Properties, and then look at the Display tab.