Select all order not respected about alferd-spritesheet-unpacker HOT 1 OPEN

public static List<Rectangle> OrderBoxes(List<Rectangle> boxes, Enums.SelectAllOrder selectAllOrder, Size spriteSheetSize)
        {
            List<List<Rectangle>> listsOfBoxes = new List<List<Rectangle>>();
            bool found = false;

            List<Rectangle> returnedOrder = boxes.OrderBy(w => w.Y + w.Height).ToList();
            foreach (Rectangle box in returnedOrder)
            {
                foreach (Rectangle compareBox in returnedOrder)
                {
                    // Find a rect on the same Y axis.
                    if (box.Top < compareBox.Bottom && box.Bottom > compareBox.Top)
                    {
                        found = false;
                        // Look for a list containing the matched rect.
                        foreach (List<Rectangle> groupedList in listsOfBoxes)
                        {
                            // Add our rect to a list we found.
                            if (groupedList.Contains(compareBox))
                            {
                                groupedList.Add(box);
                                found = true;
                                break;
                            }
                        }

                        // No list was found, create a new list and put the rect in it.
                        if (found == false)
                        {
                            List<Rectangle> newList = new List<Rectangle>();
                            listsOfBoxes.Add(newList);

                            newList.Add(box);
                        }
                        // We found a rect, stop searching for others.
                        break;
                    }
                }
            }

            // Begin to sort all of the lists by the X axis and dump into a single list.
            List<Rectangle> properOrder = new List<Rectangle>();

            foreach (List<Rectangle> groupedList in listsOfBoxes)
            {
                List<Rectangle> orderedList = groupedList.OrderBy(w => w.X).ToList();
                properOrder.AddRange(orderedList);
            }

            return properOrder;
        }