How to find the origin of variable in Drupal
Looks like you should debug the code not in theme but in the module.

I assume you use the metatag module. It adds all the metatags in metatag_html_head_alter().

Check what is your front page. If it is a View of a Panel, metatags are handled in a different way.

In the metatag module you can specify separate tags for the front page - check this setting. It might override your content metatags.