I fixed this by editing the monitors.xml file in your .config folder. You can see a more detailed description with example here...Ubuntu 11.10 dual monitor set up instructions

But briefly you can try this:

1. Open up a terminal (ctrl+alt+t)


2. Go to your config folder (cd ~/.config)


3. Open up your file for editing (gedit monitors.xml)


4. Your 2 monitors will be listed here, find the monitor on the left, it will have the values of <x>0<x> and <y>0<y>.


5. These values are measured in pixels, position the other monitor in relation to this using the x and y values. The current values you see here will be values that represent the incorrect set up when you log in - you can use them as a reference point.

This will hopefully fix it for you too.