When I was using the Box Selection Tool in Blender 2.49 (Front View) to select a corner, this was what I got: http://cl.ly/23e666443680d86dc94e - Blender selected both corners, which was very good. In Blender 2.53 it doesn’t work that way.
The best way for not to miss whatever vertices you want to select in ortographic views is to turn on Wireframe mode, by hitting the Z key. But, if you still want to select in Shaded mode, make sure you deactivate the ‘Limit selection to visible’ button in the header of the 3D View.