On rare occasions, installing Mapfolio may lead to changing your Configurable app settings, and access to your application templates.
Follow the below steps to correct this.
Click "Edit Settings"
Click the "Map" tab
Check the box in "Configurable Apps" which reads "Share the Esri default configurable apps to this group when you click Save."
Click "Save" at the top of the page.
After performing these steps and saving, make sure to clear your browser cache (ctrl + F5) and verify that you once again have access to your custom templates.