I just want to confirm my understanding of the issue. Are you going to the Replication page and selecting the Replication icon under the “Scope” column for that particular database? Or, are you just going to the general File–>Replication–>Options for this Application?
On the Replication page, when clicking the icon under the “Scope” column in the row for that particular database, it should bring up the Replication Options specific for that database. For example, for my Address Book, when I click on the Icon under the “Scope” column, the box that comes up is titled “Replication Options for Adams’s Address Book”, and from there, I can set my Replication Options explicitly for my Address Book.
I have not tested the Replication options with the Synchronize Contacts, but I would expect the functionality to be as I outlined above.