Custom Build Not Enabled?

So as the title suggests I have created a custom kodi 17 build, I have taken the files that are needed in order to install it back via my wizard.

However…Huh

After I input my repository and install my Kodi 17 build it does not ‘enable’ the skin or the addons, I find that I have to enable these back in order for the build to work.

Can anyone shed some light into what the issue is and how I can correct it so that once I install my Kodi 17 build it’s fully enabled from installation?

Kind Regards