Hi Chris, that's the trick. The problem I was having was assuming the sync would run against the tables in VCS only without any explicit inclusions or exclusions. What was happening was that the default behaviour was every single table was syncing when I used /Include:identical. When I didn't use it, the exe returned an error code when no changes were required which broke my CI build.
As soon as I removed the black-list and added a white-list, the excluded tables no longer synced as per your suggestion. It's a little bit odd - tables will sync unless there's a white-list they don't appear in - but it has answered the question. Thanks!
And yes, I'm using SQL Source Control 2 EA. I've written about this and the above question in part of a larger post here: http://troy.hn/hTh4yc