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Which client makes the query? Is it the pi OR another client?
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Possible firewall problem?
From a windows machine, that uses pihole DNS, run:
w32tm /stripchart /computer:0.debian.pool.ntp.org /dataonly /samples:5
result should be something like:
Tracking 0.debian.pool.ntp.org [51.38.2.120:123].
Collecting 5 samples.
The current time is 18-Jun-19 6:51:26 AM.
06:51:26, -02.7711642s
06:51:28, -02.7722184s
06:51:30, -02.7719083s
06:51:32, -02.7728847s
06:51:34, -02.7728659s