Perfect, thank you. From that video, I can see that your mouse clicks are falling through the Finder window for unknown reasons. When this happens with a Chrome window behind the Finder window, this fall-through click is activating the Chrome window, so it looks like the Finder window is disappearing.
Obviously, this shouldn’t be happening, and I can see from your first video that this only happens when TotalFinder is running. I haven’t yet reproduced this issue, but I have some questions:
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What’s the exact version of OS X you’re running?
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Would you mind disabling “Show sidebar icons in color” in TotalFinder’s preferences to see if the issue still happens?
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Are you using anything that might modify mouse events? Anything like a special driver for your mouse or an app like BetterTouchTool?
Steve