Hi Malcom,
I would suggest disconnecting all your external monitors, and then rebooting. Allow the console to fully boot up into Eos leaving all the external monitors still disconnected. Now exit to the welcome screen and re-connect all your external monitors. Once all the monitors are connected and powered on, try using the "Monitor Arrangement..." tool and be sure to click "Apply" even if everything looks correct.
On a side note - in Eos 1.4, there is an "Advanced" monitor setup dialog, where you can tweak all monitor settings manually.
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