Configuration->Index Listing

Where is the code for the Admin->Configuration->Index Listing located? I have turned all of the settings for "Show New Products" etc. to ON, but I lost those.
They show up when I switch back to the default template. They disappeared when I was trying to do the new security updates and I although I've tried to UNDO everything with backups, I can't figure out how to get products back on the Index Listing Page.
I am using 1.3.8a. The client was already hosted with GoDaddy.
I must have altered the code somewhere but I can't find where. Any clues?
Thanks!

If they show on Classic and not on your custom template, then your custom template is either not calling the files or they are commented out etc.

Can you tell me the name of the file where that code exists?

Several files are affected depending on the navigation of the categories:
tpl_index_default.php
tpl_index_categories.php
tpl_index_product_list.php

see if those are in your templates and overrides and if so, do a comparison of those to the original files ...

Thank you so much for your timely response. None of those files are in my template overrides. I'll keep searching.