Preserve call stack of, Timer.schedule in java

I have a daemon thread running which calls a function (prepareOrder) whenever the cook is not busy and there are orders to be delivered. The prepareOrder calls the orderComplete function after a certain interval of time depending upon the time required to complete the order. Now the problem i am facing is only the last call to the prepareOrder gets displayed on sout.

The daemon

package ui;
import Model.takeOrderModel;
public class daemonThread extends Thread{
    //call this method in the main method of driving fucntion
    private  takeOrderModel orderModel;
    daemonThread(takeOrderModel orderModel){
        this.orderModel = orderModel;
    }
    public void assignCook(){
        while(true){
            int toComplete = orderModel.toCompleteOrders.size();
            if ( !orderModel.cookBusy && toComplete>0 ) orderModel.prepareOrder();
        }
    }
}

The prepare order function.

 public void prepareOrder(){
    // pick the last element from list
    if (toCompleteOrders.size() > 0){
        String nextPrepare = toCompleteOrders.get(toCompleteOrders.size()-1);
        order orderToComplete = allOrdersPlaced.get(nextPrepare);
        completeOrder(orderToComplete);
        toCompleteOrders.remove(nextPrepare);
        }
    }

    //Helper function to prepareOrder moves an order from toComplete to prepared order
    private void completeOrder(order orderToComplete){
        changeCookState();
        new java.util.Timer().schedule(
                new java.util.TimerTask(){
                    @Override
                    public void run() {
                        changeCookState();
                        preparedOrders.add(orderToComplete.id);
                        deliverOrder(orderToComplete.id);
                    }
                }, (long) (orderToComplete.timeToComplete*60)
        );
    }

    public void changeCookState(){
        this.cookBusy = !cookBusy;
    }

    // MODIFIES removes a order from the prepared list and puts it in delivered list
    public String deliverOrder(String completedOrder){
        preparedOrders.remove(completedOrder);
        deliveredOrders.add(completedOrder);
        System.out.println(String.format("The order of %s is here", allOrdersPlaced.get(completedOrder).customerName));
        return String.format("The order of %s is here", allOrdersPlaced.get(completedOrder).customerName);
    }

The main function driving code.

orderMachine.takeNewOrder(fullMeal, "Tom");
orderMachine.takeNewOrder(halfMeal, "Bob");
daemonThread backThread = new daemonThread(orderMachine);
backThread.setDaemon(true);
backThread.assignCook();

Now for me only the last placed order("Bob") gets printed on sout. How can all calls created by Timer.schedule stay in stack.

Edits

The take new order function.

public boolean takeNewOrder(List<item> itemsInOrder, String customerName){
        try {
            order newOrder = new order(itemsInOrder, customerName);
            allOrdersPlaced.put(newOrder.id, newOrder);
            toCompleteOrders.add(newOrder.id);
            return true;
        } catch (Exception e) {
            e.printStackTrace();
            return false;
        }
    }

Edit 2

here is the public repo containing the complete code
https://github.com/oreanroy/Share_code_samples/tree/master/takeOrder

The problem in this code is a concurrency bug - the cookBusy variable is being written to from two different threads. To fix this, use an AtomicBoolean instead of a boolean, as this is thread safe.

AtomicBoolean cookBusy = new AtomicBoolean(false);

Use compareAndSet to ensure the shared variable is set to a known value before updating it.

    public void changeCookState(boolean busy){
        if (!this.cookBusy.compareAndSet(!busy, busy))
        {
            throw new RuntimeException("shared variable set to unexpected value");
        }
    }