Forgive the potential thread hijack - but I get very similar issues using nVidia Control Panel.
One computer insists (and refuses to be taught) that the screen on the left is actually on the right, and vice-versa. So mousie goes off the left edge of the left screen to appear on the right edge of the right screen (picture it).
I can switch them - until I click "OK", then they switch back.
TimS - are you sure you are still in "Dual Monitor" mode and that it hasn't switched itself to "Single Monitor" again and splitting the whole image into two halves. (Didn't explain that very well, but *I* know what I mean, lol).