Java - Caso 3 no me entra en el bucle y el caso 5 no me ordena bien

import java.util.Arrays;

import java.util.Scanner;

public class Banco2 {

	public static void main(String[] args) {

		//Scanner construction

		Scanner Entrada=new Scanner(System.in);//Scanner used to read Strings

		Scanner ent=new Scanner(System.in);//Scanner used to read Integer variables

		//----------------------------------------------------------------------//

		//Variables used for the problem

		int sucursales=0;

		int options;

		int numsucursal;//Variable used for the case 1

		int numbempleados;//Variable used for the case 1

		int numeroempleado=0;

		String surname;

		String empleados;//Variable used for the case 2

		String Apellido;//Varible used for the case 3

		int numeroempleadototal=0;//Variable used as a counter in the case 4

		//--------------------------------------------------------------------------------//

		//We ask the user for the number of branches

			System.out.println("Introduce el numero de sucursales");

			sucursales=ent.nextInt();

		//We read the number of branches that the user introduces

		//Construction of our multidimensional array

		String banco [][]=new String[sucursales][];

		// i rows, j columns

		//In this loop we fill in the position

		for (int i=0;i<banco.length;i++) {

				System.out.println("Introduceme la cantidad de empleados que trabajan en la sucursal " + ( i+1 ));

				numeroempleado=ent.nextInt();

			//We assign it to the object bank

			banco[i]=new String[numeroempleado];

		}

		//We are going to fill in the array

		for (int i=0;i<banco.length;i++) {

			for(int j=0;j<banco[i].length;j++) {

					System.out.println("Introduceme el nombre de los empleados " + ( i+1));//We use i+1 to know the branches that the user is filliing in

					banco[i][j]=Entrada.nextLine();

			}

		}

		//--------------------------------------------------------------------------------------------------------//

		do {

		//Menu options

		System.out.println("Ingrese una de las opciones que desea hacer");

    	System.out.println("1.Sacar por pantalla todos los empleados de unas sucursales");

    	System.out.println("2.Sacar por pantalla a qué sucursal pertenece un empleado");

    	System.out.println("3.Sacar por pantalla cuántos empleados hay con el mismo primer apellido");

    	System.out.println("4.Sacar por pantalla cuántos empleados hay en total en el Banco.");

    	System.out.println("5.Saca por pantalla todos los empleados del centro ordenados alfabéticamente.");

    	//We read the option introduced

    	options=ent.nextInt();

    	switch(options) {

    		case 1:

    			System.out.println("Introduce la sucursal del empleado");

    			numsucursal=ent.nextInt();//We read the branch introduced by the user

    			System.out.println("Introduce el numero del empleado");

    			numbempleados=ent.nextInt();//We introduce the number of the employee that we want to know

    			//We print out our multidimensional array formed by the number of branch and number of employees, taking into account that the number of the branch as it moves will disminish a position

    			System.out.println("El empleado es " + banco [numsucursal-1] [numbempleados]);

    		break;

    		case 2:

    			System.out.println("Dime el nombre del empleado");

    			empleados=Entrada.nextLine();//We read the employee that the user has introduced

    			//We go through the array to know the worker of the branch

    			for (int i=0;i<banco.length;i++) {

    				for (int j=0;j<banco[i].length;j++) {

    					//We make and if to compare the employee name introduced by the user with the employees introduced previously before the menu options

    					//equalsIgnoreCase  ignores the case while comparing two strings.

    					if(empleados.equalsIgnoreCase(banco[i][j])) {

    						//We print out the branch that the employee belongs to

    					System.out.println("El empleado pertenece a la siguiente sucursal: " + (i + 1));

    				}//end of the second for

    			}//end of the first for

    		}

    		break;

    		case 3:

    			//We ask the user for the surname

    			System.out.println("Dime el apellido del empleado");

    			//We read the surname introduced by the user

    			Apellido=Entrada.nextLine();

    			//We do two loops in order to go through the array

    			for(int i=0;i<banco.length;i++) {

    				//No me entra al bucle

    				for (int j=0;j<banco[i].length;j++) {

    					surname=banco[i][j].substring(banco[i][j].indexOf(""),+1);

    					//We assign it to the variable Apellido

    					surname=Apellido.substring(0,Apellido.indexOf(""));

    					if(Apellido.equalsIgnoreCase(surname)) {

    						System.out.println("Los empleados con el apellido que quieres saber son: " +banco[i][j]);

    					}

    				}

    			}

    		break;

    		case 4:

    				//We use to loops to go through the array

    				for (int i=0;i<banco.length;i++){

    					for (int j=0;j<banco[i].length;j++) {

    						//We create a new variable used as a counter of the positions of the array

    						numeroempleadototal ++;

    						//We print out the number of the counter

    						System.out.println("Este es el numero total de empleados que hay en las sucursales " + numeroempleadototal);

    				}

    				}

    		break;

    		case 5:

    			//We create the array with the names to order

    			String ordernames[] = new String[numeroempleadototal];

    			Arrays.sort(ordernames);

    			for(int i=0;i<ordernames.length;i++) {

    				System.out.println("Nombre"+ordernames[i]);

    			}

    			break;

    		default:

    		System.out.println("Ha elegido usted la opcion incorrecta");

    		break;

    	}

		}while(options!=6);

	}//end of main

}//end of class