Repeatable: Always
Steps to repeat:
1. Install Drupal with metatag and features modules.
2. To 'Node' add (under 'Advanced')' to 'CANONICAL URL' the value '[node:url]'.
3. Export this to a feature.
4. Drop and recreate the database, reinstall.
5. Go to features admin page.

Expected Results:
I see my feature with status 'Default'.

Actual Results:
I see my feature with state 'Overridden'.

OS: Ubuntu 12.10
Database: 5.5.28-0ubuntu0.12.10.2
Web Server: Apache/2.2.22 (Ubuntu)
PHP 5.4.6-1ubuntu1.1
PHP error_reporting = E_ALL
Drupal 7.19

Comments

I'm experiencing a similar issue.

I created a User feature where I exported User fields, metatags, etc. On a fresh install I enable the metatag module and the Users feature. It's showing as overridden due to the metatag with no option to revert.

If I use Drush to revert the feature it's still showing as overridden.

The diff module can be useful to see what differences it thinks there is. Also check the issue queue of that module