Hi Matt,
It is very important that the featureGuid remain the same. If you do a manual install it is generated for you, but if you then change to use a featureDefinition file it is up to you to make sure the generated guid is the one you add to the feature definition. If it is a different guid then it will not affect the instance that was added previously from a manual install. Also if you accidentally re-use a guid from another feature by copying an existing featureDefinition, then settings you add will go the feature that matches the guid.
For this reason, it is important when making features that you plan to package to always use a feature definition file from the beginning and generate a new featureGuid to go in your featureDefinition. Then it will always have the same featureGuid in every installation whereas manually installed features will have a random guid.
Hope it helps,
Joe