How about this for a temporary solution: make a button on your bookmarks bar (assuming that you have it shown, otherwise this tip is useless), name it something like "center" or whatever, and then put the following bit of Javascript code in the address field:
javascript:window.resizeTo((screen.width-0),(screen.height-50));window.moveTo(0,0)
Just copy and paste the code above. Now, next time Safari opens a new window which is offset to the right relative to the right corner of the screen, hit the button and your window will pop into place.
Elegant it ain't, but it works...
EDIT: for one reason or another, the board misinterprets the bit of code above: please REMOVE the space between java script to javascript