The Permissions class effectively ignores UnresolvedPermissions for a given class that are added after an actual instance of the class is added or passed to implies.  Demonstrated with this test program:

import java.security.*;

public class Test {

    public static class FooPermission extends BasicPermission {
	public FooPermission(String name) {
	    super(name);
	}
    }

    public static void main(String[] args) throws Exception {
	Permissions pc = new Permissions();
	pc.add(new FooPermission("foo"));
	pc.add(new UnresolvedPermission(FooPermission.class.getName(),
					"bar", null, null));
	if (!pc.implies(new FooPermission("bar"))) {
	    System.out.println("first test failed");
	}
	pc = new Permissions();
	pc.add(new UnresolvedPermission(FooPermission.class.getName(),
					"foo", null, null));
	if (!pc.implies(new FooPermission("foo"))) {
	    throw new RuntimeException("oops");
	}
	pc.add(new UnresolvedPermission(FooPermission.class.getName(),
					"bar", null, null));
	if (!pc.implies(new FooPermission("bar"))) {
	    System.out.println("second test failed");
	}
    }

}