Windows 7 Problems with programs in windows 7 not responding

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Disgraceful

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Recently I have been having a random problem that started about a week ago. I run Warcraft III windowed mode and I have not had a problem with it. It isn't just warcraft anymore so I posted this here. Anyways, when I click inside the window while things like Warcraft III or Mozilla Firefox are running, it freezes for about half a second. It happens about every third click, and sometimes Firefox goes nuts and flashes continuously for 30 seconds or so. When this happens I very briefly see my desktop before it flashes back. This can be very annoying because when I click something and it stops responding briefly, I have to click the thing again. This happens VERY frequently, however does not effect Warcraft while not playing in windowed mode. It is not the 3rd party mouse application I installed (Logitech Setpoint) because when I uninstalled that the problem still occurs. I am not sure what this is because MBAM (Malware-bytes) and an online scan did not dectect any viruses. Is anyone else getting this problem? Or does anyone have a solution to it?
 
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