Just in case others experience this, one of the 13 nodes I upgraded last night (the central node in fact) experienced a long delay at around the section where it installs/upgrades the management services.
I noted that queue.manager process was utilising 100% cpu and the system was totally bogged down.
Initially i assumed that the queue manager process was hung when i stopped the services to do the upgrade, so I performed a kill -9 on it (silly me i know).
After the installation then succeeding, every restart of the scalix services resulted in the queue.manager process still utilising 100% cpu, and no services starting.
I then ran the installer again and performed the upgrade of all components. This time I just waited for the queue manager to complete, and everything was fine.
So, just a word of warning to anyone else who sees this, the install may take a while and the queue manager might go nuts, but just leave it alone until it completes.