I recently purchased Menu Pro because I need to posistion the menu. But when I am on the Items tab of the builder, and try to edit the "Edit menu
Settings" section, it will not allow me to change the "Menu Hor. Offset " or the "Menu Ver. Offset".
I couldn't reproduce the problem you described, but in worst case you can adjust the values in the resulting menu files. The position is first values in block_top and block_left array (vertical and horizontal coordinates respectively).
I have this problem as well.