I'm using a Macbook Air with an external monitor (I finally converted from Windows, don't know what took me soo long ;-) ).
When I have a Chrome browser window open in the external monitor and click a link that opens in a popup, the popup will open hidden on my Macbook. I can't find a setting to open it in the same window my browser is in.
A few times I even had a pulldown open in a different window. Weird ...