What works for me is "grabbing hold" of one of the corners and dragging it to enlarge the window. Then do the same with the opposite corner. Then go to File->Close, rather than closing the window with the X. Next time I open a window, it's that size.
However, I never right click on links to open a new window as you describe, so I cannot say if that situation is different. Presumeably there's a need for you to open links in that manner?
Cheers
bug