See also: LUCENE-2666.
It appears that a server restart fixes this problem, implying that some cache is not being cleared.
This may be the result of a search being performed at index time, causing a lucene cache to be loaded that is not correctly invalidated when the index has been built?

We need to try and reproduce this locally, and also do an audit of all Lucene IndexReaders and ensure they are being correctly closed, or reopened after an index.commit();,