Steps to reproduce:
Create two features, each with at least 2 variants of the same page.
Change one of the variants
drush fua -y
Expectation: Nothing is overridden.
Reality: The features are marked as overridden.
Then, just to compound everything:
drush fra --force -y
Pick one of the features that is STILL marked overridden
drush fd THAT_FEATURE
It will report that nothing is overridden.