Noisy sound data when recording 16 bit. Anyone experience this?

Question

I'm working on a program that displays a spectrogram and it works just fine with 8-bit audio, but not so well with 16-bit. In the 16-bit data there's an incredible amount of noise that isn't present in the 8-bit data. Oddly, the noise is present across the entire range of frequencies I'm reading. If it makes a difference, I've only tested this on Vista. Here is an abbreviated code snippet:
ArrayList<double[]> wave = new ArrayList<double[]>();
int sampSize = audioFormat.getSampleSizeInBits();
numBytesRead = targetDataLine.read(data, 0, data.length);
wave.add(new double[dataSize]);
if (sampSize == 16) {
      for (int i = 0; i < numBytesRead / 2; i++) {
            wave.get(wave.size()-1) = (double) ((data[2*i+1] << 8) | data[2*i]);
} else if (sampSize == 8) {
for (int i = 0; i < numBytesRead; i++) {
wave.get(wave.size()-1)[i] = (double) data[i];
//perform fft on wave data

Answer 1

Alright. I've created an "sscce" as suggested, and managed to keep it just under 20KB. It's pretty self explanatory but I will describe it briefly:
The program graphs the waveform of data read from a microphone. Two graphs are displayed. The top graph displays the data read in 8-bit form, and the bottom graph reads the data in 16-bit form. I wasn't sure if it was possible to read in 8-bit data and 16-bit data from the same source simultaneously, so you have to toggle between them. Clicking in the graph area will pause/unpause that graph, allowing the other graph to run. Pausing both graphs allows for the data to be compared side-by-side.
This image illustrates my problem: http://yfrog.com/3d8vs16graphj. The data was recorded during silence, so what you see is purely noise. The 16-bit data clearly has plateaus that aren't present in the 8-bit data. I believe these "plateaus" are the cause of the broad spectrum of noise in my fft results. If anyone is interested, please test my code by copying and pasting directly into a new project:
package sscce16bit;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Image;
import java.awt.Insets;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.awt.geom.Rectangle2D;
import java.util.ArrayList;
import javax.sound.sampled.AudioFormat;
import javax.sound.sampled.AudioSystem;
import javax.sound.sampled.DataLine;
import javax.sound.sampled.TargetDataLine;
import javax.swing.BorderFactory;
import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.SwingWorker;
public class sscce extends JPanel {
    static MainThread mainThread;
    static final int gh = 100;
    static final int gw = 300;
    static final int ch = 40;
    static final int labw = 60;
    static final int cw = gw;
    static final Dimension graphSize = new Dimension(gw, gh);
    static final Dimension labelPSize = new Dimension(labw, gh);
    static final Dimension controlsSize = new Dimension(cw, ch);
    static final Dimension panelSize = new Dimension(gw + labelPSize.width + 20,
                                            2 * (labelPSize.height + ch));
    static GraphPanel graph8;
    static GraphPanel graph16;
    static ControlsPanel cPan;
    int procCounter = 0;
    int curArrayPos = 0;
    TargetDataLine targetDataLine8;
    TargetDataLine targetDataLine16;
    //double maxAmpShown = -1.0d;
    //double MAX_AMP = 0.0d;
    ArrayList<double[]> wave = new ArrayList<double[]>();
    boolean pauseProc = false;
    //graph display controls
    int tickMarkLen = 8;
    int numOfLabels = 5;
    //audio format
    AudioFormat audioFormat8;
    AudioFormat audioFormat16;
    int dataSize = 1024; //buffer size = 2^10 (line buffer size is 4000 typically);
    final int dataSampleSize = dataSize;
    final float sampleRate = 8000.0F; //8000,11025,16000,22050,44100
    final int sampleSizeInBits8 = 8; //8 or 16
    final int sampleSizeInBits16 = 16;
    final int numofchannels = 1; //1 or 2
    final boolean signed = true;
    final boolean bigEndian = false;
    public sscce () { //constructor
        audioFormat8 = new AudioFormat(sampleRate,
                sampleSizeInBits8, numofchannels, signed, bigEndian);
        audioFormat16 = new AudioFormat(sampleRate,
                sampleSizeInBits16, numofchannels, signed, bigEndian);
        this.setPreferredSize(panelSize);
        this.setMinimumSize(panelSize);
        this.setMaximumSize(panelSize);
        this.setBorder(BorderFactory.createLineBorder(Color.black));
        this.setLayout(new GridBagLayout());
        GridBagConstraints gbc = new GridBagConstraints();
        gbc.insets = new Insets(0, 0, 0, 0);
        gbc.anchor = GridBagConstraints.CENTER;
        graph8 = new GraphPanel(sampleSizeInBits8,
                audioFormat8, targetDataLine8, true);
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.gridwidth = 1;
        add(graph8.labP, gbc);
        gbc.gridx = 1;
        gbc.gridy = 0;
        gbc.gridwidth = 1;
        add(graph8, gbc);
        cPan = new ControlsPanel();
        gbc.gridx = 1;
        gbc.gridy = 1;
        gbc.gridwidth = 1;
        add(cPan, gbc);
        graph16 = new GraphPanel(sampleSizeInBits16,
                audioFormat16, targetDataLine16, false);
        gbc.gridx = 0;
        gbc.gridy = 2;
        gbc.gridwidth = 1;
        add(graph16.labP, gbc);
        gbc.gridx = 1;
        gbc.gridy = 2;
        gbc.gridwidth = 1;
        add(graph16, gbc);
        mainThread = new MainThread(this);
        mainThread.execute();
    } //end constructor
    class ControlsPanel extends JPanel {
        ControlsPanel() {
            this.setPreferredSize(controlsSize);
            this.setMinimumSize(controlsSize);
            this.setMaximumSize(controlsSize);
        @Override
        public void paint(Graphics g) {
            String pause8, pause16;
            String zoom8, zoom16;
            Rectangle2D textR[] = new Rectangle2D[6];
            if (graph8.pauseGraph) {
                pause8 = "paused";
            } else {
                pause8 = "running";
            if (graph16.pauseGraph) {
                pause16 = " paused,";
            } else {
                pause16 = " running,";
            zoom8 = " " + Double.toString(graph8.MAX_AMP / graph8.maxAmpShown) +
                    "x zoom";
            zoom16 = " " + Double.toString(graph16.MAX_AMP / graph16.maxAmpShown) +
                    "x zoom";
            String text[] = new String[] { "8bit: "+ pause8 + zoom8,
                                        "16bit: " + pause16 + zoom16 };
            for (int i = 0; i < text.length; i++) {
                textR[i] = g.getFontMetrics().getStringBounds(text[0], g);
            textR[0].setRect(0, textR[0].getHeight(),
                    textR[0].getWidth(), textR[0].getHeight());
            textR[1].setRect(cw / 2.0d, textR[1].getHeight(),
                    textR[1].getWidth(), textR[1].getHeight());
            for (int i = 0; i < text.length; i++) {
                g.drawString(text, (int) textR[i].getX(), (int) textR[i].getY());
class GraphPanel extends JPanel implements MouseListener{
double maxAmpShown = -1.0d;
double MAX_AMP = 0.0d;
boolean pauseGraph = false;
AudioFormat audioFormat;
CaptureThread capThread;
TargetDataLine targetDataLine;
LabelsPanel labP;
ArrayList<Integer> labels = null;
boolean setLabels = true;
boolean stopped = true;
Image bImage;
Graphics bg;