Any chance you get more informations by following the procedure for
time-admin at https://wiki.ubuntu.com/DebuggingGnomeSystemTools? As I
really don't see how the gnome-system-tools could be at fault here, you
may first check that 'sudo restart ntp' doesn't trigger the same issues.

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Computer reboots when enabling/disabling ntp
https://bugs.launchpad.net/bugs/511205
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