I have checked the mouse settings to make sure that the mouse does not activate a window merely by hovering (that box is unchecked) and I have installed a new mouse and a new keyboard and made sure that my USB drivers and mouse-drivers are up-to-date. I have also disabled anti-virus. I have also made sure that devices do not participate in any power-management scheme (that option is grayed out in any event). But nothing seems to fix this problem.
This problem occurs in both regular mode and Safe Mode.
And here's the problem described in greater detail:
Sometimes when I click on a partially obscured window, it does not become the active window. The partially obscured window could be running almost anything -- Notepad, Microsoft Money, a browser, there's no pattern there. And yet sometimes when I allow the mouse merely to hover over a partially obscured window, it comes forward, just like the task bar/auto-hide toolbar will pop out from "behind" the monitor when the mouse moves over its region on the edge of the screen. When the partially obscured window doesn't come forward when clicked, it's just like the topmost window has been opened like a "modal dialog".
Here's how I temporarily fix this problem: Ctrl-Alt-DEL and then click the CANCEL button to return to the desktop. NOTE, the CANCEL button always takes two clicks. On the first click it does not respond. When I return to the desktop, things function as they should, for a few minutes.
A gazillion people have reported this problem -- there's a thread on Microsoft Technet about it-- but the MSFT techies there are blaming it on defective hardware --a malfunctioning mouse/keyboard or bad motherboard. I've changed out the mouse and keyboard, but I cannot swap out the motherboard. However, I have run the M/B manufacturer's diagnostics which report that the USB ports are working correctly, FWIW.
The properties tabs in Device Manager also all say that the devices are functioning properly.
This has been going on for over a week and is driving me up the wall, since it happens every few minutes. I hope someone here has a bright idea about how to fix it.