I don't know LCD setups, but your problem sounds like it is caused by your screen resolution (for the LCD) being smaller than the virtual desktop resolution (for the X server). This will create some scrollable space on the desktop, you can scroll left and right with your mouse on the 'virtual desktop' that is too large for your LCD.
To fix this you might have to force your virtual desktop resolution to match whatever resolution you're getting with the WXGA LCD. The X server has a variable in the config for setting the virtual desktop size. It is:
Virtual xsize ysize
see the man page for XF86Config, in the Display subsection: