Problem: I have a features install in my development instance and my production instances. I create new fields in both and then want to merge the features back into one. I download the feature from production, copy the files to my development instance, and revert the feature. Now the fields I created in my development instance are now inactive because they are not apart of the feature.
Solution: Disable and reenable the feature and all the modules that come with CCK.
That's the short answer. Thanks to this thread http://drupal.org/node/335597