Don't know if you've tried this as a bandaid changing the clock source might 
help. I recently found a small group of servers that chose tsc as the clock 
source. While using tsc the system clock would lose 1 second every 30 seconds. 
Switching to hpet as the clock source (well technically all the others worked) 
would stabilize the clock and thus ntpd wouldn't lose its mind. 
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