Given that you have a large number of zones and programs, to isolate the possible causes of the problem, I suggest that you temporarily set the number of zones to a smaller one (like 16), and reboot, and see if this makes any difference. I personally can’t reproduce the issue you are seeing — I’ve imported your configurations on a test OS 2.3 and I don’t see any NTP or timing issue. But I wonder if the problem maybe due to the rather large number of zones and programs, such that when accessing the controller, transferring this amount of data is triggering some buffer overflow problem that we haven’t discovered, and that in turn affects NTP. The easiest way to test is to make the number of zones smaller, so that when you access the controller, the data remains small. At least this is worth a try since I otherwise have no clue why this is happening.