This bug may be video card related. My systems with this bug :
Emachines with Trigem Computer Motherboard, 1.2GHz Celeron, Nvidia MX4000 64MB 
PCI video card
PC Chips A15G Motherboard, 2.2GHz Athlon 64, Nvidia  GeForce 8600GT 512MB PCIE 
video card
Micron PC Millenia GS Motherboard, Intel PIII 866MHz , Nvidia Riva TNT2 Model 
64 32MB AGP video card

When I replace the Emachines Nvidia MX4000 card with a S3 Virge (86c325)
video card, the bug is not present

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xubuntu compositor does not distinguish inactive windows
https://bugs.launchpad.net/bugs/317193
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