Ok, so it seems the bug only happens when building with maven from the command line, never when running the test from inside Eclipse. Probably because of the use of HashMaps in our internal code, which makes the relative order of fields change from one run to another.

Anyway, I think I got the issue: provided IDs were being handled incorrectly for @IndexedEmbeddeds . It turns out it had nothing to do with Elasticsearch after all, and we may currently have issues with the Lucene backend too (for example, provided IDs being erased by an embedded provided ID).
I'll submit a PR soon.