Make sure your output directory and input directory do not overlap. These are mine. Also build the production instance before you do the native build. Mine went from over 10 MB to less than 2 MB.
I had the same problem with the old SDK Tools.
Try using the latest SDK tools and use the "sencha app build native" for native packaging, you will need to generate a new project with "sencha app create" tough. You may run into problems migrating with the sdk tools, so copy only your files in the app folder into your new project.