Just a shot in the dark, but there is an option in Safari to open new windows in a Tab. Is it possible that is what is happening or is it possible the new window is opening behind the current window and you are simply not seeing it. I know both of these things have happened to me, especially when I am using the browser in a full screen mode.
"All you've got to do is own up to your ignorance honestly, and you'll find people who are eager to fill your head with information" --Walt Disney
