EE Always Loading Site Default Template

Question

I just did a DB upgrade from 2.4 to 2.10.1. And I switched my templates to save as files. And I am having issues where EE will always load the site default template index. I've removed Pages and Better Workflow to see if that would help. If I try to go to any page other than the site index, it loads the sites default template. The SQL Query below is ran on every template/template group I create. If I modify the query below I can get it to pull the correct template, but what is configured with EE that is making it load the site's default template/index on every other template I try to create?

SELECT `exp_templates`.*, `exp_template_groups`.`group_name`
FROM (`exp_templates`)
JOIN `exp_template_groups` ON `exp_template_groups`.`group_id` = `exp_templates`.`group_id`
WHERE `exp_template_groups`.`site_id` =  '1'
AND `exp_templates`.`template_name` =  'index'
AND `exp_template_groups`.`is_site_default` =  'y'
#APP/libraries/Template.php L:2381  EE_Template::fetch_template()

SELECT `exp_templates`.*, `exp_template_groups`.`group_name`
FROM (`exp_templates`)
JOIN `exp_template_groups` ON `exp_template_groups`.`group_id` = `exp_templates`.`group_id`
WHERE `exp_template_groups`.`site_id` =  '1'
AND `exp_templates`.`template_name` =  '.layout'
AND `exp_template_groups`.`group_name` =  'site'
#APP/libraries/Template.php L:2381  EE_Template::fetch_template()

Answer 1

In my config file I found that uri segments were being queried instead of allowing EE to automatically parse them.