I'm running Firefox 4.0, but the problem was also with 3.6. When clicking on links that open up a new smaller window displaying information on another page. The window is nearly always displayed in the top left corner of my screen and then I have to drag and reposition it to the opposite side.
This is very frustrating to have to do this. I have had the window somehow remember the last position and size, but can't reproduce the steps I did to make the change stay.
How do you get Firefox to open link to a new page windowed and in a specified location?
I think Firefox will try and instanciate windows with the same positioning and size as when it was last closed.
So try opening up Firefox, resize and position it to where you want it (not in fullscreen). Now close the browser by the close button (don't force close by killing the process). Restart Firefox and hopefully new windows will have the position and size you desire.