Ok, so it's not "keeping them in sync" as you stated in your first post, it's not a "leap second sneaking in" as in your second post. Now it is somehow data that is not labeled, and only becomes a problem during leap seconds. I'm sure you can see how changing your story and lack of details would make someone skeptical that the problem even exists.
If there really is a problem I'm really interested in hearing what it is. But it doesn't sound like you plan to be straight forward about explaining it.
Not exactly the kind of thing that causes catastrophic failure. More so the kind of thing that periodically pops up to be annoying.