I think on further investigation it was my fault all along in the end and you can close this ticket as "no repro", but it was really hard to diagnose because my System.err output was being swallowed completely - System.err.println and Logger output both simply never appearing - most peculiar.
Actually it seems there's more to it than this... I'll continue to investigate it and if I find anything concrete I'll comment.
Spurious unique index constraint violation on inserts