When importing an existing GeoServer configuration into JDBCConfig, the Catalog (stores, leayers etc) gets imported but the configuration (Service settings, contact info) does not.
I have tracked the failure down to JDBCGeoServerLoader.java:line 90. The call to config.setImport(false) here causes JDBCConfig to skip loading the configuration at JDBCGeoServerLoader.java:line 107. Removing line 90 was sufficient to fix the issue.
It looks like this change was made as part of the JDBCResource store refactoring.
Pull request here: https://github.com/geoserver/geoserver/pull/1647