Here's a temporarily fix that should work for most who have issues with the game-window and user-interface not being aligned right to screen/monitor.
Note: this fix might not work with Windows 7 (see "For Windows 7").
For Windows XP and Vista:
Right-click taskbar. Choose Properties. Untick "Keep the taskbar on top of other windows".
Boot game up.
For Windows 7:
To my knowledge Microsoft removed the "Keep the taskbar on top of other windows" option for Windows 7. Turning on Auto-hide might do the trick.
Keep in mind that this is only a temporarily fix that might not work for all. Xsyon development team is most likely looking into it.