SharePoint search not indexing contents of document libraries
check that the folder item is approved and published.
The effected libraries had the option Library Settings > Versioning Settings > Draft item security set to 'Only users who can edit items'.
My crawl account did have full control of the documents in the library and I logged in using the crawl account to confirm this.
When i changed the above option to 'Any user who can read items' then reset the index and did a full crawl, the documents where indexed and are now being served up by search.
I had previously read that the crawler ignores this option but it seems that it interprates it in an unexpected way.
Interestingly (and frustratingly) when i changed the 'Draft Item Security' option to 'Any user who can read items' and did an incremental craw
Ensure that the service account that is setup on the Search Service Application (under "Applcation Management" > "manage service applications" in Central Admin) has the correct permissions to view the documents. Also ensure that this account is not too highly privileged to ensure private documents are not displayed in the search results. I would recommend setting up a service account called “spsearch”, which has read access granted to the content sources.