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What you describe looks like a loss of window focus. Sometimes some stupid background programs that pop up a new windows for a fraction of a second cause this. After such windows close, your window does not get back the focus until you either hit Alt+Tab, or click with the mouse in it.
Go look for such unusual programs. I guess you are using Microsoft Winodws. Look for a tool named "sysinternals autostarts". You can use this tool to find out any programs that start automatically on your system, and you can temporarily disable each of those (you should know what you are doing and how to recover from it).
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