Ok so I changed my context on my jira server to /jira (I had to authenticate a number of time and it was annoying me).
NOTE: My jira and confluence are installed on the same machine and use the JIRA authentication database.
When restarting confluence I could not log in.. bummer
I updated the JIRA reference in the admin console and still no joy so I looked in the logs: /var/atlassian/application-data/confluence/logs for me.
I was getting this error:
com.atlassian.crowd.exception.InvalidCrowdServiceException: The following URL does not specify a valid Crowd User Management REST service: http://server:8080/rest/usermanagement/1/event
So I logged into the db and changed in the ATTRIBUTE_VALUE column to the correct new server context http://server:8080/jira in CWD_DIRECTORY_ATTRIBUTE table where the ATTRIBUTE_NAME was crowd.server.url.
Fixed my problem right up.