Elasticsearch 1.0 changed the API relating to the mappings and settings endpoints. This means that in the Elasticsearch Setup page in the control panel, mapping optimization and stemming configuration changes do not appear to be applied. However, they are being applied; they are just not being read back correctly. The fix for this issue (visual appearance only) is attached as a unified diff file. If you don't upgrade to ES 1.0, you will not run into this issue.