Any new templates I include are not being recognized. In the error message below, CallToActionFF1.ss definitely exists under templates/includes. The only way to have Silverstripe recognize new templates is to manually delete cache files (specificallly in templatemanifest). I've tried flush=all, flush=1 and dev/build but none work.

Here is the portion of the template which points to the include:

<% include PageHeaderHero %>
<% include NewsUpdate %>
<% include CallToActionFF1 %>
<% include CallToActionFF2 %>

Here is my error message:

User Warning] None of these templates can be found in theme 'flip-theme': CallToActionFF1.ss
GET /
Line 786 in /Users/justinbrown/web/flip/framework/view/SSViewer.php
Source
777 
778 		if(!$this->chosenTemplates) {
779 			$templateList = (is_array($templateList)) ? $templateList : array($templateList);
780 
781 			user_error(
782 				"None of these templates can be found in theme '"
783 				. Config::inst()->get('SSViewer', 'theme') . "': "
784 				. implode(".ss, ", $templateList) . ".ss", 
785 				E_USER_WARNING
786 
			);
787 		}
788 	}
789 
790 	/**
791 	 * Set the template parser that will be used in template generation
792 	 * @param \TemplateParser $parser

I feel like my issue is similar to: http://www.silverstripe.org/community/forums/general-questions/show/25555

Figured it out. I updated from SilverStripe 3.1.8 to 3.1.9 which fixes a bug (01989aa) where template manifests weren't flushing on some environments.