Pages in the _layouts directory are not affected by changes done to Master Pages using SharePoint Designer. Sharepoint runtime always pick up things from _layouts directory for url's pointing to "_layouts" directory .
1. Try changing the background color for master page for your site using SharePoint Designer.
2. Go to site main Default.aspx. You will see the change in background color as the master page has been unghosted and resides in Content DB.
3. Click the site settings page and navigate to site settings page. The deafult background theme color is retained.