Not an unity/compiz issue I will tell.
I have the same thing if I try, like you setting a high resolution on my 
external monitor (1600 x 900), no issue if both are using 1024x768. Either 
related to hardware performance or driver then. Reassigning to mesa

** Changed in: unity
       Status: Confirmed => Invalid

** Changed in: unity (Ubuntu)
       Status: Confirmed => Invalid

** Package changed: compiz (Ubuntu) => mesa (Ubuntu)

** Changed in: mesa (Ubuntu)
       Status: Confirmed => New

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https://bugs.launchpad.net/bugs/769650

Title:
  dual monitor runs unusably slow (Asus 1000HE, Intel 945GME)

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