The same was with Gizmo and Bubba. Giz is 11lbs and Bubba was 1 1/2lb. At first Giz would run from him afraid and hide. Then he went thru a "this is my house" stage and nipped at him..after a month now they are best buds. Has really made a pup of Gizmo again.
Give it some time. They'll make their way.