Re-install settings application.
System application are odexed, which means the code part it extracted and kept separate and also some crucial parts of the application are kept in framework.jar. If you want to copy your freshly-compiled application to your phone, you have to deodex it first, which restores the missing parts and only then you may replace /system/Settings.apk with your new file. And, please, make sure you delete old /system/Settings.odex file, otherwise it won't work.

As usually, it's recommended to save old Settings.apk/odex files just in case when something goes wrong.