I've have the same problem.
I go into amdcccle (Administrative), change to dual monitor setup and click 
apply. Change happens immediately and everything works. I then reboot and the 
change has reverted and I'm back to cloned screens.
Device is a Radeon HD 4850
Drivers/Software
fglrx - 2:8.723.1-0ubuntu2
fglrx-amdcccle - 2:8.723.1-0ubuntu2
fglrx-kernel-source - 2:8.660-0ubuntu6 
xorg-driver-fglrx     2:8.660-0ubuntu4

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amdcccle settings do not persist lucid
https://bugs.launchpad.net/bugs/551475
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which is subscribed to fglrx-installer in ubuntu.

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