Not sure I understand. What is being displayed in these windows that pop up and cause the game window to minimize?
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Got to be something running in the background, no one else has reported anything like this. I would check for Virus and Spyware.
I don't know really what to tell you, no one else has reported it so it has to be unique to your system. You say it never happened until you installed a user made mod, Perhaps that mod altered something, and you have not completely removed the mod from your system now that you went back to vanilla.