Display arrangement behaves strangely

I have a Macbook Pro with 2 1280x1024 monitors attached, one with a DVI out cable and one with a DisplayLink adapter via USB. All seems to work fine for most arrangements, however in the display arrangement gui ins system preferences I am getting an inconsistent result. When I try and put the laptop screen beneath the DVI attached monitor and set the dock to be on the DVI monitor, it actually appears in reality on the laptop screen. If I move it under the other monitor it works fine.
So I am getting a different result to what is being displayed in the arrangement window

Desktop?
Do a backup.
Go to Finder and select your user/home folder. With that Finder window as the front window, either select Finder/View/Show View options or go command - J. When the View options opens, check ’Show Library Folder’. That should make your user library folder visible in your user/home folder. Select Library. Then go to Preferences/com.apple.desktop.plist. Move the .plist to your desktop.
Re-launch Finder by restarting and test. If it works okay, delete the plist from the desktop.
If the same, return the .plist to where you got it from, overwriting the newer one.
Thanks to leonie for some information contained in this.

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john199527
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Display arrangement behaves strangely

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