Apparently jackson + friends make assumptions when it comes to parsing raw -> ZonedDateTime. It appears that the ZonedDateTime for createInstant when deserializing timestamps are not being handled properly somehow, so you need custom code. We have our own Jackson serializer and deserializer for ZonedDateTime to ensure we always get milli in and milli out.
Here's the code (Apache2 license) and the maven repository links if it's helpful.