I have been logging certain network messages on a few PCs (WinXP and RH8) and I noticed that on the RH8 machine, the logged time drifts and then jumps back into synchronisation at about 4:01 a.m. every morning.

I have found where the system clock is set to hardware clock (clock --hctosys) during init, but how is the syncing performed at 4:01 am?

crontab schedules cron.daily tasks for 4:01 or 4:02 every morning, but I can't sets the actual command which sets system time to hardware clock time.

What command / instruction / whatever is used to do the daily synchronisation of system clock to hardware clock?

cron has multiple ways to be scheduled:

/etc/crontab
/etc/cron.d/<files>
/var/spool/cron/<user_files>

Typically /etc/crontab will be the one that executes /etc/cron.daily (and cron.hourly and cron.monthly etc...). Within those directories (cron.daily etc...) there are files for various purposes.

You need to look for the command in each of those directories. Note that the syntax is not the same in each of these. Type "man cron" and "man crontab" for more details.

As a quick check you can type "crontab -l" to see if you have it in /var/spool/cron/root file.