Hello Nigel,
Thanks very much for upgrading to v6.
Am I right in thinking that you have Windows configured to launch Hauptwerk automatically as a the PC boots?
The error can occur as Windows boots if Windows launches Hauptwerk before Windows has launched (or finished launching) the iLok software.
See this topic for a solution (a script to delay launching Hauptwerk a little): viewtopic.php?f=4&t=19289&p=144937