Abstract base class with multiple subclasses. Some subclasses have additional properties in DetailXXX tables. DB lacks FK relationships. Relationships are mapped on "natural" composite keys.

FNHMappingExample.cs

// Component is an abstract base class
// Weld inherits from Component
// Weld has additional properties in DetailWeld table

    public class ComponentMap : ClassMap<Component>
    {
        public ComponentMap()
        {
            Table("Component");
            CompositeId().KeyProperty(x => x.ItemId).KeyProperty(x => x.RevNo);
            // Properties mapped here
            DiscriminateSubClassesOnColumn("ComponentTypeId", 4);
         }
    }

    public class WeldMap : SubclassMap<Weld>
    {
        public WeldMap()
        {
            DiscriminatorValue(8);

            Join("DetailWeld",
                 wd =>
                     {
                         wd.KeyColumn("ItemId");
                         wd.KeyColumn("RevNo");
                         //More properties mapped here

                     });
        }
    }

With this, I get:

NHibernate.FKUnmatchingColumnsException : Foreign key (FK5BB087E7E43D7E5D:DetailWeld [RevNo])) must have same number of columns as the referenced primary key (ComponentMaster [ItemId, RevNo])

I assume if you swap the two wd.KeyColumn lines around the exception changes to be ... (...:DetailWeld [ItemId])? That would certainly indicate that the second call is overwriting the first.

Are you using the master version or the 1.1 binary?

Yes on swapping the order of calls to KeyColumn.
FNH is 1.1 binary (1.1.0.685)