I am comparing constraints on two of my schemas. The source schema has FK constraints that are enabled and the target schema has some FK constraints that are disabled. The compare shows them as different and adds a statement in the sync script to validate the target constraint, but there is not a statement that enables the target constraint.
Option needs to be selected to compare status.
In the Schema Compare window, check the 'Compare object status' option, which is located on the Options | Object Type Specific Options tab.