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For your first issue, personally I would use daemon running instead of cron running the job. Running update using cron will run cron process in addition to your ntp as well increasing the load on your system.
Configure and use ntpd to maintain the time. This is what ntpd is MADE for, while ntpdate is to test/report the time on a remote machine (and optionally set the local clock to match).
During boot, there may be some advantage in running ntpdate PRIOR to the ntpd startup so that the clock is correct when ntpd starts.
Just because you can drive a screw with a putty knife does not make it the right tool for the job. We often stop searching for solutions when we find one that works, but we SHOULD search to find the RIGHT tool. In this case you have two 'right' tools, but for different parts of the job.
ntpdate to set the clock once, ntpd to maintain time sync continuously.
I have no clue why ntpdate would leave any gap in the clock settings. Were it on my machines I would check the TZ updates and settings, and then the clock drift and offset settings.
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