Have you tried adjtimex? It's a helper application for ntpd.
After upgrading an FC3 system to FC5, ntpd just had no luck
getting the clock to sync. There had been no problem when
the box was running FC3. But on FC5, ntpd repeatedly logged
error messages about servers being unreachable.
Recently, in the this mailing list, I saw some posts about adjtimex
and installed it. adjtimex will make suggestions for tick and frequency
offsets to adjust the system clock. I ran adjtimex on two succesive
days, chose a value for tick based on the results, and put a line in
/etc/rc.d/rc.local to set the tick value.
adjtimex --tick 9960
To my delight, the FC5 system now syncs within 12 to 15 minutes
of booting the system.
I'm not going to take the time to investigate, but the area I would look
into if I was more motivated, is the values for CONFIG_HZ and
CONFIG_HZ_250. These are set for my kernel, 126.96.36.199 from
kernel.org. Perhaps they were different for FC3, or not set at all.
Bottom line - adjtimex helped my FC5 system get back to normal
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