The menu table is rendered with a 2px gap around it, in other words, the top edge of the menu does not come flush with the bottom of the header, and the left edge of the menu is not flush with the right edge of the middle column, the way it is on your site.

Increasing the $template_default["nav_table_struct"]["space_right"] just makes the menu width larger but does not remove the approx. 2px gap around it.