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1. Export a sub-set of metatags into a feature.
2. Enable the feature in another database.
3. Attempt to override the sub-set >> values stay with the global ones.
The above occurs because the exported metatag configuration contains the cid ($conf->cid) but it is not saved in the database, so when the overriden configuration is about to be saved, metatag_config_save() sees that there is a $cid and calls drupal_write_record() for update.
I have seen that deleting the cid values at the feature fixes it, but wonder if removing the cid when exporting a feature may cause other side-effects.