You might expect that when you want to create a custom Master Page that you can just make a copy of the “default.master” Master Page and customize from there. After all, it is the default Master Page that is used on every site out-of-the-box, so it should be a good starting point.
Unfortunately this is not the case. After using a customized copy of the default Master Page it was noticed that publishing pages, in particular those in Wikis, were not being indexed in search. While these pages appeared normally in the browser, the search logs were displaying the message “Content for this URL is excluded by the server because a no-index attribute”. Poor English aside, this error message completely fails to identify the problem.
Further investigation shows that while the pages pull up fine using the Intranet site URL, they do not pull up when using the server name for the site as defined in the Alternate Access Mappings and as used in the indexing process. Changing the Master Page for the site to one of the various out-of-the-box options fixes the problem.
If you open up the default.master Master Page and the OrangeSingleLevel.master Master Page in SharePoint Designer and compare the Register commands at the top of the code you will notice that OrangeSingelLevel.master has quite a few that are not in default.master. Most of these revolve around Publishing. Copy these to your custom Master Page and it should now be viewable via the server name and indexed properly.