This also happens for me. Laptop screen 1024x768; External screen 1280x1024
I'm using an HP NC6210 laptop with the new intel driver.
This is still happening with the latest packages as of today. Unfortunately
this is a showstopper for me and prevents me using Compiz.
** Changed in: compiz (Ubuntu)
Status: New => Confirmed
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Gutsy: Compiz full screen not correctly calculated
https://bugs.launchpad.net/bugs/130933
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