Score in replay missions
I can confirm that I have also replayed a campaign mission, and the High score and Best Medal did not register after the replay.
In the Campaign, there is a button for "Play Unlocked Missions". For each of the completed missions you should see a list of Played Seeds, as well as a High score and Best Medal for each replay. However, in my experience, there have been a number of times when only the first playthrough registered in this list, and a few times when none of the playthroughs registered in this list.
This appears to be buggy or inconsistent behavior of the game. After attempting to diagnose the problem (by quitting a mission halfway through, exiting the game suddenly during a mission, and fully completing a mission), whether a replay shows up or not in the list of Played Seeds was still inconsistent.
This applies to the Offline Campaign for the May 2012 edition of Frozen Synapse.