I always assumed that when the documentation for the JavaScript window.open said that the "height" argument "Specifies the height of the window, in pixels" that it meant the height of entire parent window (the one with the "X" in the upper-right corner) not the client-size of the browser control window!  The same is true of the "width" argument. (at least we're consistent!) 

So, if you're worried about the positioning and sizing of a popup window be sure to account for the size of your status bar, toolbar, and outer border of your window.  They all 3 affect how window.open is (or should be) handled.