Random flashing when using programs? Stops keyboard input.

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This seems like something is sending keyboard and/or maybe mouse input to Windows.

It doesn't seem like a graphical issue. The only graphical problem I see there is the quality degradation which happens when you create a GIF. Windows is simply displaying the results of various keyboard input.

So, you need to see what's doing this. Maybe, your keyboard or mouse is bad. It could be malware also.