I have done an
and let it do its thing - analysing the top on an terminal and looking at the logfiles to see what processes are closing off, obvious that the once the process causing the issue shuts down the re-boot will speed-up.
All the services stopped, took loooong time from 15:13 to last entry in syslog at 16:01, almost an hour (48 minutes!) the last standing processes was called from ISPConfig clamscan
All the time the HDD seem to run non-stop!