Missing Box File Names in Layout Controller for Template Aberdeen Neutral

[fribble]

I have Aberdeen Neutral template on two diff websites: cottoncreekcargo.com and 40acrefarms.com
Host is hostgator, php version is 4.3.8
I noticed when working on the 40acrefarms site several of the Box File Names are missing under Layout Controller. The only ones there are: currencies_header.php, languages_header.php, search_header.php, what's_new.php, reviews.php, aberdeen_neutral/information.php, search.php, shopping_cart.php, specials.php, and who's_online.php

I am not having this problem on cottoncreekcargo.
I tried reinstalling the default Zen template and then going to check layout-boxes controller again. When I do the screen appears as follows:

http://www.40acrefarms.com/images/te...IMG_9984RS.jpg

this is an image of the screen when I have aberdeen_neutral.php installed

http://www.40acrefarms.com/images/te...IMG_9985RS.jpg

It is obvious I have corrupted a file somewhere or something. I have made many customization so I really did not want to delete everything and start over with a fresh install, but I can't even set my categories to show up since I am missing so many of the boxes.

Any help appreciated.

[fribble]

I think I have this resolved now.

[mc12345678]

I think I have this resolved now.

Mind sharing how with the class? What was wrong, etc?