I'm having similar problems. When trying to do a dual-box setup with a single monitor, using a window layout where both screens are full-screened except the task bar, I end up with the UI taking up only about the left two third of the screen while the non-UI portions of the display (in-game rendered things) are correct. That means that the right portions of the UI are more or less in the middle of the screen, instead of on the left.
http://oi40.tinypic.com/o2vj5.jpg is an example
I noticed that the settings file had lines that said:
Height = 1212
NativeHeight = 1170
NativeWidth = 1920
Width = 1170
So I tried adjusting the Height and Width to match the other values (1170 and 1920), but they simply got ignored and reset when I quit the game again. If I set the height to something less than 1170 it's closer to correct, but there are weird graphical glitches at the bottom of the screen.
I also tried clear out all the settings files and starting from scratch, to no avail.
So far, no success in resolving the issue.