Some more research shows that I am not even entering the setup loop, here 
is my class that contains the applicationhelper for the IOIO:

package com.tukajo.ioiograph;

import android.app.Activity;
import android.app.Application;
import android.content.Context;
import android.widget.Toast;

import ioio.lib.api.AnalogInput;
import ioio.lib.api.IOIO;
import ioio.lib.api.IOIO.VersionType;
import ioio.lib.api.exception.ConnectionLostException;
import ioio.lib.util.BaseIOIOLooper;
import ioio.lib.util.IOIOLooper;
import ioio.lib.util.IOIOLooperProvider;
import ioio.lib.util.android.IOIOAndroidApplicationHelper;

public class customIOIO extends Application implements IOIOLooperProvider {

globalControlInstance globalData = globalControlInstance.getInstance();
public AnalogInput pin39;
public AnalogInput pin40;
public AnalogInput pin41;
public AnalogInput pin42;
public AnalogInput pin43;

public float currentPin39Voltage = 0;
public float currentPin40Voltage = 0;
public float currentPin41Voltage = 0;
public float currentPin42Voltage = 0;
public float currentPin43Voltage = 0;

private final IOIOAndroidApplicationHelper helper_ = new 
IOIOAndroidApplicationHelper(
this, this);

protected void create(Context myContext, Activity myActivity) {
helper_.create();
//Toast.makeText(getBaseContext(), "IOIO Connected", 
Toast.LENGTH_LONG).show();
}

protected void destroy() {
helper_.destroy();
}

protected void start() {
 helper_.start();
}

protected void stop() {
helper_.stop();
}

protected void restart() {
helper_.restart();
}

class Looper extends BaseIOIOLooper{
@Override
protected void setup() throws ConnectionLostException{
pin39 = ioio_.openAnalogInput(39);
pin40 = ioio_.openAnalogInput(40);
pin41 = ioio_.openAnalogInput(41);
pin42 = ioio_.openAnalogInput(42);
pin43 = ioio_.openAnalogInput(43);
showVersions(ioio_, "IOIO connected!");
}
@Override
public void loop() throws ConnectionLostException, InterruptedException{
currentPin39Voltage = pin39.getVoltage();
currentPin40Voltage = pin40.getVoltage();
currentPin41Voltage = pin41.getVoltage();
currentPin42Voltage = pin42.getVoltage();
currentPin43Voltage = pin43.getVoltage();
}
}
@Override
public IOIOLooper createIOIOLooper(String connectionType, Object extra) {
return new Looper();
}

public float getCurrentPin39Voltage() {
return currentPin39Voltage;
}

public void setCurrentPin39Voltage(float currentPin39Voltage) {
this.currentPin39Voltage = currentPin39Voltage;
}

public float getCurrentPin40Voltage() {
return currentPin40Voltage;
}

public void setCurrentPin40Voltage(float currentPin40Voltage) {
this.currentPin40Voltage = currentPin40Voltage;
}

public float getCurrentPin41Voltage() {
return currentPin41Voltage;
}

public void setCurrentPin41Voltage(float currentPin41Voltage) {
this.currentPin41Voltage = currentPin41Voltage;
}

public float getCurrentPin42Voltage() {
return currentPin42Voltage;
}

public void setCurrentPin42Voltage(float currentPin42Voltage) {
this.currentPin42Voltage = currentPin42Voltage;
}

public float getCurrentPin43Voltage() {
return currentPin43Voltage;
}

public void setCurrentPin43Voltage(float currentPin43Voltage) {
this.currentPin43Voltage = currentPin43Voltage;
}
private void showVersions(IOIO ioio, String title) {
Toast.makeText(getApplicationContext(),(String.format("%s\n" +
"IOIOLib: %s\n" +
"Application firmware: %s\n" +
"Bootloader firmware: %s\n" +
"Hardware: %s",
title,
ioio.getImplVersion(VersionType.IOIOLIB_VER),
ioio.getImplVersion(VersionType.APP_FIRMWARE_VER),
ioio.getImplVersion(VersionType.BOOTLOADER_VER),
ioio.getImplVersion(VersionType.HARDWARE_VER))),Toast.LENGTH_LONG).show();
}


}


On Friday, August 1, 2014 9:19:54 AM UTC-5, Tim Frisch wrote:
>
> I am trying to connect to an emulator through the PC (I've gotten this to 
> work before)
>
> Anyway, the board is having trouble setting up for some reason.
>
> I get thousands of 
> 03-07 14:00:21.063: D/IOIOImpl(13885): Waiting for IOIO connection
> 03-07 14:00:21.063: V/IOIOImpl(13885): Waiting for underlying connection
> 03-07 14:00:21.063: V/SocketIOIOConnection(13885): Creating server socket
> 03-07 14:00:21.063: D/IOIOImpl(13885): Physical disconnect.
> 03-07 14:00:21.063: D/IOIOImpl(13885): Connection lost / aborted
>
> The application launches correctly; and my "ioio" instance is created, I 
> followed the globalioio pattern that was found here:
>
> https://groups.google.com/forum/#!msg/ioio-users/PlalZY9qse0/CoYF5IawGy4J
>
> Any ideas what could cause this?
>
> Sorry if it's too vague.
>

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