First of all, thanks for all the replies. Some useful suggestions in there which I'll be trying this morning.
2008/10/17 Mikkel L. Ellertson <mikkel infinity-ltd com>
runs "/sbin/hwclock --utc --hctosys" to sync the hardware clock toBut this is syncing the system clock to the hardware clock, not the
the system clock.
hardware clock to the system clock. This has me confused as to what
Sorry, my mistake. I meant to say "to sync the system clock to the hardware clock". As Todd Denniston pointed out, the hardware clock can be significantly more accurate than the system clock. Our application requires accurate time but some users are not net-connected so can't use NTP. If NTP is in use we sync the hardware clock to the system clock once per hour. If NTP is NOT in use, we sync the system clock to the hardware clock once per hour.
The reason to sync the hardware clock to the system clock when using NTP is to ensure that the difference never gets too great, so if there is a power outage or unclean shutdown, the hardware clock is reasonably accurate when it comes back up.
We always used to do this on our old RedHat 7.3 based systems without problem. We recently updated to F9 and this issue appeared so maybe some kernel changes have brought the issue to light.
I've checked /var/log/messages and root mail but there's nothing of any interest in there.
I just tried running the script at runlevel 3 with the sync occurring every 1 second. It failed after 461 syncs but there was no output of any interest, just a hung screen.
I'll try some of the other suggestions a bit later.