Comments - millisecond part is trimmed away when saving Java Date obj by hibernate
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This is perhaps a multilevel-issue. That server supports microseconds is good, but you also need clients support microseconds. In this case it would be JDBC driver that needs support for microseconds. I do not know the current state of Connector/J, but you can check with pure JDBC calls (store and retrieve e.g java.sql.Timestamp with fractional seconds)
Hibernate is yet another level which theoretically can lose milliseconds, I have not looked at it closely though, and do not know if there is anything that can be done in Hibernate configuration.