Burraq(main)

public class Burraq extends MapActivity {

  long start;
	long stop;
	
    @Override
    public void onNewIntent(Intent intent) {
    super.onNewIntent(intent);
    setIntent(intent);
    Log.d("MapActivity","Got new Data again");
    setMaptoProvidedLocation();
    } 
    
    
	@Override
    public void onCreate(Bundle savedInstanceState) {
        super.onCreate(savedInstanceState);
        setContentView(R.layout.activity_burraq);
    
		setMaptoProvidedLocation();
    
    }
    
 
    // Setting Google Map to provided location 
     private void setMaptoProvidedLocation() {
    	 //Default position
         String LON =  "33.651686";
         String LAT =  "73.156333";
     	
         if(SmsReceiver.chk==1){
             Intent i = getIntent();
             LAT =  i.getExtras().getString("NewLat");
             LON=  i.getExtras().getString("NewLon");
         }
 
 		MapView mapView = (MapView) findViewById(R.id.themap);
 		MapController control = mapView.getController();
 	    
 		mapView.setBuiltInZoomControls(true);  
 	    Touchy t = new Touchy();
        List<Overlay> overlayList = mapView.getOverlays();
        overlayList.add(t);
        
       //Map Animate to new GeoPoints
        
     		double lat = Double.parseDouble(LON); // latitude
     		double lon = Double.parseDouble(LAT); // longitude
     		GeoPoint geoPoint = new GeoPoint((int) (lat * 1E6), (int) (lon * 1E6));
     		control.animateTo(geoPoint);
     		control.setZoom(100);
     		Toast.makeText(getApplicationContext(),
     				"Your Location is - \nLat: " + lat + "\nLong: " + lon, 0)
     				.show();

     		}
}

SmsReceiver

package com.robot.burraq;


import android.content.BroadcastReceiver;
import android.content.Context;
import android.content.Intent;
import android.os.Bundle;
import android.telephony.SmsMessage;
import android.widget.Toast;
 
public class SmsReceiver extends BroadcastReceiver
{
  // setting global variable.
	public static String up_lon;
	public static String up_lat;
	public static int chk =0;

    @Override
    public void onReceive(Context context, Intent intent) 
    {
        //---get the SMS message passed in---
        Bundle bundle = intent.getExtras();        
        SmsMessage[] msgs = null;
        String str = ""; 
        String str2 = ""; 
	
        //fetching message string
        if (bundle != null)
        {
            //---retrieve the SMS message received---
            Object[] pdus = (Object[]) bundle.get("pdus");
            msgs = new SmsMessage[pdus.length];            
            String sender_num = null;
			for (int i=0; i<msgs.length; i++){
                msgs[i] = SmsMessage.createFromPdu((byte[])pdus[i]);                
               // str += "SMS from " + msgs[i].getOriginatingAddress(); 
              //  str += " :";
                str = msgs[i].getMessageBody().toString();
            //   str += "\n";        
                
                 sender_num = msgs[i].getOriginatingAddress();
                     
			}
			
			//Divide message string to 2 parts longitude and latitude by detection "," 
			int flag =0;
			str2 =str.substring(3,4);
			up_lon = "";
			up_lat = "";
			for(int j=0; j<str.length();j++)
			{			
				str2 =str.substring(j,j+1);
				if(flag == 1)
				{
					up_lat += str2;
				}
				if(str2.equals(","))
				{
					flag = 1;
				}
				if(flag == 0)
				{
					up_lon += str2;
				}
			}
			
				  chk=1;
				  
				  //New Location fetched
				  Toast.makeText(context,up_lat + up_lon , Toast.LENGTH_SHORT).show();
       	 
				  Intent i = new Intent();
				  i.putExtra("NewLat", up_lat);
				  i.putExtra("NewLon", up_lon);
        }   
        
    }
}

where are you starting Burraq activity in SmsReceiver ?
Please modify the code as per bellow -

//New Location fetched

Toast.makeText(context,up_lat + up_lon , Toast.LENGTH_SHORT).show();

final Intent intent = new Intent(context, Burraq.class);
i.putExtra("NewLat", up_lat);
i.putExtra("NewLon", up_lon);
context.startActivity(intent); // I can not find this in you code ...

Now , First time , if you get sms , It would start Map activity...
Second time , If Map activity is in forground and still you get sms in background ,
It would again restart the activity...!!

Its good to know that your code is working now...
Now , you can handle some things like -----

1. Handle map display for frequent sms ( like map is not loaded and you get new sms again )
2. Sms authentication and validation .
3. Overlay zoom in and zoom out ...so ..It can feel user that location has been changed ...

One more thing...please don't forget to vote up answer in stack overflow , so It would be useful in future for other guys like you...:)

4. Even apart from SMS ,you can use other cheaper ways ...like GCM ( Push notification )...

anyways ..its your choice... :)