I've noticed that the server names that get inserted into the comments at the top of generated scripts are backwards.
E.g., it always says "Run this script on ServerB.my_db - This database will be modified to synchronize it with ServerA.my_db" when I am in fact trying to modify ServerA.my_db
E.g., it always says "Run this script on ServerB.my_db - This database will be modified to synchronize it with ServerA.my_db" when I am in fact trying to modify ServerA.my_db