I have installed Magento 2.1.1 and created a Custom Theme by using the following procedure:
1) Copied the theme-frontend-luma theme from Vendor > Magento folder
2) Pasted in app/design /frontend/<Custom>/<Theme>
3) Modified the three files theme.xml, registration.php and composer.json as required
4) Changed the custom theme in magento backend : Content > Design > Configuration
But after enabling the template path hints, it was still showing the paths from vendor/module-theme... not from My Custom Theme.
Can any one try to solve this.. Please suggest any solution..
Can you please share your theme.xml and registration.php file code?
Main theme file declaration are goes under theme.xml and registration.php file.
May be you have did some mistakes in above file and your changes are not applied.