When we persist domain.xml in full, the elytron subsystem ends up being reordered vs what we shipped in the standard config. I assume this occurs with all the config files.

The element and attribute order in the standard config, the persistence and the xsd should be the same.

Specifically:

audit-logging moves from after providers to before
http moves from before sasl to after

The xsd agrees with what's in the standard config so this looks to be a marshalling problem.