When you create a feature it is best to use a feature definition file and you must use a unique guid for the featureGuid. If you installed the feature manually a feature guid was generated in the page and if you later add a feature definition you must use the same feature guid there.

When you add a new setting in the featureDefinition file the setup page will add the setting, but if the featureGuid is not correct it end up installing it as a new feature rather than updating the existing one and things get out of sync. You may want to compare the feature guid in the database mp_FeatureDefinitions table vs the one in the featureDefinition file and the one on the instance of your feature in mp_Modules.

Note that the setup page and the featuredefinition file only sets the default settings, it does not update existing instances if you change the default setting value, it only makes it so that newly created instances will get the new default value. 

Hope that helps,

Joe

If your feature is in a custom project, your feature definition file should also be on your project and copied by your post build event into /Setup/applications folder

When you make any changes in your code you need to build your project again so the updated files get copied again by the post build event.

The setup page is working correctly, it is used the same for all mojoPortal included features as well as all add on products. If it isn't working for you then you are not doing something correctly. You should make sure the the copy of your feature definition file under Web/applications/[yourfeaturename]/FeatureDefinitions is the correct updated version and has no mistakes or missing items. The copy that you edit should be in your own project.

You should also as I mentioned before look in the mp_Modules table, find the row for your instance of the feature that doesn't have the correct settings and make sure it has the correct feature guid. Please double check it. 

Myself I never install features manually I always use feature definition files and they always work, going back and forth between manual and feature definition installation is not a good idea.

You can study the post build events and feature definition files in mojoPortal.Features.UI and WebStore.UI to learn more.

Also if there are any mistakes in your featuredefinition file it could be throwing errors that would be logged. ie things like declaring an ISettingControl type of setting with an incorrect path to the control or an error occurs in the control itself would also cause it to fail to load in the feature settings page.

Once setup runs and creates the key/value pairs for a feature's settings, they are stored in the database. This thread is a little older but should have good information for you about uninstalling/reinstalling a feature.

Jamie