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I have included some JavaScript in a master page of a site collection that shows a button. When an internal user clicks the button it directs to an internal accessible site and when an external user clicks it directs to an external accessible site.

This works perfectly with all browsers without any errors. But when I click Site Settings on any of my sites in my site collection the button disappears.

This happens only in Site Settings. I have included the correct master page in the Site Settings so there is no issue with that.

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There are two master pages for each site like Site Master Page and System Master Page. When you go to the site settings page, then SP applies System Master Page. So make sure both master pages are same.

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Your both master pages may be same, then alternate css could the issue for hiding your button.

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