I'm having a similar problem... my symptoms are, with time, my system responsiveness to window changes starts to crawl. When I try to change window focus my various desktop windows start to flicker, darken, brighten, etc. Clicking on an application in the taskbar to switch foreground focus seems to be very sluggish, if it happens at all.
I haven't noticed a specific pattern as to when this happens, but it always seems like it takes the computer being active for some time. Often, when I come back to the computer in the morning (running all night) I have this problem.
For me, to correct the issue I have been able to goto the system tray and bring up the WindowFX settings. Then I toggle WindowFX off/on and everything seems to work OK.
HP Quad core i7 laptop.
Intel HD Graphics 3000; Dual monitors