This problem only happened in a recently installed instance after restoring a database dump that had (possibly) a different timezone from the running server, so that the table contents got created with a future timestamp, that led to a unexpected behavior on the com.atlassian.confluence.search.lucene.queue.DatabaseIndexTaskQueue where the '<CONF_HOME>/index/.timestamp' file was created with a date in the future. The consequence was that every time the indexing job ran it couldn't retrieve the new items on the queue to be indexed, resulting in a instance where no content was automatically indexed.
A workaround was re-indexing manually, a definitive solution was correcting the timestamps on the table, removing the '.timestamp' file and restaring the instance.

Some debug info available at: https://studio.atlassian.com/browse/JST-3712

Workaround

http://confluence.atlassian.com/display/CONFKB/Confluence+Fails+to+Process+Index+Queue+Automatically