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Explorer.exe acting strange

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About once a day, my computer has been doing something strange: The icons and taskbar disappear, leaving only the wallpaper. After a second, the icons and taskbar return and the items in the sytem tray reload one after the other, similar to what happens when you get an error that crashes explorer.exe (but without an error message). This hasn't happened while working with programs, only when messing with folders on the desktop.

Also, the desktop icons "flicker" as if they are being refreshed every five minutes or so. Normally, I would brush this off, but I recently was hit with some malware that Crustyoldbloke helped me clear using ewido and HJT. Part of the malware were some gambling and adult icons that would refresh within five minutes of being deleted. The icons are gone, but the refreshing seems to still be happening. Is this periodic "refresh" a leftover effect of malware? Currently I'm running a (hopefully) clean system with SBS&D, AA SE, and ewido.

Any ideas? Thanks.
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