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If you have ad blocking on, links clicked in gmail will also be blocked. Check the status bar at the very bottom of the window for a small square window icon with an X in it. That indicates a pop up was blocked and it could be your link. Click on the icon and select an item in the pop up menu and a new window will open. I still have issues when I force Google to open new windows in a new tab instead. Usually, I get the new tab and a new window of the same link. It will also break the "Pop Out" option in a gtalk chat within gmail.