Reading Options Not Displaying

I am using 2.3.1 for a client company CMS site. Because there is no blog on the site (only about 100 hierarchal pages – 3 levels deep) I customized the admin section (to have client logo and colors as well as) to hide any references to posts and categories. I did this by simply commenting out the specific unwanted menu items in wp-admin/menu.php. While adding content I also selected a static page in “Reading Options” to become the home page.

Recently I went back to the “Reading Options” page, and it is not displaying anything except a button that says “Update Options” which when pressed takes me to a table of variables (options.php).

I have tried deactivating all plugins, as well as reinstalling all the original wp-admin files and still the page does not display reading options.

THEN, I tried installing filosofo homepage control ( http://www.ilfilosofo.com/blog/home-page-control/ ) and it is not able to display any of my pages as options.

Any thoughts?