Averaging Grades: getting 0's instead of user input

Question 1

Here's the corrected code which solves your issues.

There were two major issues, you were using a local array grades instead of your static global array grades. (So remove the declaration from main)

Secondly, you were never inserting the first value integerInput which caused the first element to be lost.

       import java.awt.*;
    import javax.swing.*;
    import javax.swing.text.*;
    import java.text.DecimalFormat;

    class AverageGrades extends JFrame {
        // construct conponents
        static JLabel title = new JLabel("Average of Grades");
        static JTextPane textPane = new JTextPane();
        static int numberOfGrades = 0;
        static int total = 0;
        static DecimalFormat twoDigits = new DecimalFormat("##0.00");

        // set array
        static int[] grades = new int[50];

        // create content pane
        public Container createContentPane() {
            // create JTextPane and center panel
            JPanel northPanel = new JPanel();
            northPanel.setLayout(new FlowLayout());
            northPanel.add(title);

            JPanel centerPanel = new JPanel();
            textPane = addTextToPane();
            JScrollPane scrollPane = new JScrollPane(textPane);
            scrollPane
                    .setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
            scrollPane.setPreferredSize(new Dimension(500, 200));
            centerPanel.add(scrollPane);

            // create Container and set attributes
            Container c = getContentPane();
            c.setLayout(new BorderLayout(10, 10));
            c.add(northPanel, BorderLayout.NORTH);
            c.add(centerPanel, BorderLayout.CENTER);

            return c;
        }

        // method to add new text to JTextPane
        public static JTextPane addTextToPane() {
            int counter = 0;
            Document doc = textPane.getDocument();
            try {
                // clear previous text
                doc.remove(0, doc.getLength());

                // insert title
                doc.insertString(0, "Grades\n", textPane.getStyle("large"));

//BREAKING IF NUMBER IS 0, SIGNIFIES THAT ALL ELEMENTS ARE COVERED
//counter IS USED TO CALCULATE THE TOTAL NUMBER OF ELEMENTS
                // insert grades and calculate average
                for (int j = 0; j < grades.length; j++) {
                    if (grades[j] != 0) {
                        doc.insertString(doc.getLength(), grades[j] + "\n",
                                textPane.getStyle("large"));
                        counter++;
                    } else {
                        break;
                    }
                }

//THIS LINE INSERTS THE AVERAGE IN THE PANEL
                doc.insertString(doc.getLength(), "Average is :"
                        + (total / counter) + "\n", textPane.getStyle("large"));

            } catch (BadLocationException ble) {
                System.err.println("Couldn't insert text");
            }

            return textPane;
        }


//CORRECT THE SORTING FUNCTION
// THE SORTING SHOULD BE IN REVERSE ORDER FOR YOUR REQUIREMENTS

        // method to sort array
        public void grades(int grdArray[]) {
            // sort int array
            for (int pass = 1; pass < grdArray.length; pass++) {
                for (int element = 0; element < grdArray.length - 1; element++) {
                    swap(grades, element, element + 1);

                }
            }
            addTextToPane();

        }


        // method to swap elements of array
        public void swap(int swapArray[], int first, int second) {
            int hold;
            hold = swapArray[first];
            swapArray[first] = swapArray[second];
            swapArray[second] = hold;
        }

        // execute method at run time
        public static void main(String args[]) {
            JFrame.setDefaultLookAndFeelDecorated(true);
            AverageGrades f = new AverageGrades();
            f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

            // accept first grade
            int integerInput = Integer.parseInt(JOptionPane.showInputDialog(null,
                    "Please enter a grade (0-100) or -1 to calculate the average"));

            // while loop accepts more grades, keeps count, and calulates the total
            int count = 0;
            grades[0] = integerInput;
            count++;
            int num = 0;
            while (count < 50 && num != -1) {
                num = Integer.parseInt(JOptionPane.showInputDialog(null,
                        "Please enter a grade (0-100) or -1 to calculate the average"
                                + (count + 1)));

//USING TOTAL FIELD TO CALCULATE SUM
                if (num != -1) {
                    grades[count] = num;
                    total += grades[count];
                }



                count++;

            }

//CALL THE SORTING FUNCTION AFTER CORRECTING IT

            //f.grades(grades);

            // create content pane
            f.setContentPane(f.createContentPane());
            f.setSize(600, 375);
            f.setVisible(true);

        }
    }

Question 2

You are defining your grade array twice: once inside your class:

static int[] grades = new int[50];

then in main():

int[] grades = new int[50];