Curiously the problem has gone away. What happened was I knocked together a tiny webapp to try and deploy that as a test. It deployed cleanly and unlike the main EAR which also deployed cleanly it showed up in the Console Runtime section.
I tried the EAR again and this time it failed to deploy due to a dependency issue because of the use of Hibernate 5.1 in WF 13. I fixed this issue and now the EAR deploys and runs.
Sorry I can not provide any explanation for this and I am pretty sure I made no configuration changes to have caused this change in behaviour. Hopefully this might help anyone else coming across this oddity..