JavaScript - Extension Stops Executing After Reaching Some Page

  <script language="JavaScript">
var HAS_EXPIRED = 'Time has Expired!';
var IS_NONE = 'None';
function secondCountdown(s){
	
	if(s){
		
		var timeleft = document.getElementById('timeleft').innerHTML;
		
		if((timeleft == HAS_EXPIRED) || (timeleft == IS_NONE)) return false;
		
		timeleft = timeleft.replace('<font>', '');
		timeleft = timeleft.replace('</font>', '');
		
		var time = timeleft.split(":");
		
		var secs = time[2] * 1;
		var mins = time[1] * 1;
		var hrs = time[0] * 1;
		
		secs += (mins * 60) + (hrs * 3600);
		secs -= 1;
		
		if(secs <= 0){
			
			document.getElementById('timeleft').innerHTML = HAS_EXPIRED;
			return false;
			
		} else {
			
			hrs = Math.floor(secs/3600);
			secs -= (hrs * 3600);
			
			mins = Math.floor(secs/60);
			secs -= (mins * 60);			
							
			if(hrs < 10)	hrs = '0' + hrs;
			if(mins < 10)	mins = '0' + mins;			
			if(secs < 10)	secs = '0' + secs;
					
			document.getElementById('timeleft').innerHTML = hrs + ':' + mins + ':' + secs;
			
		}
		
	}
	
	setTimeout('secondCountdown(true)',1000);
	
}

bootloaderAdd('secondCountdown()');
bootloaderOn();

</script>

function setTimeRed() 
{
    document.getElementById("time").style.ClassName = 'timetable_r';
}

function setTimeBlack() 
{
    document.getElementById("time").style.ClassName = 'time_r';
}

function changeTimeButton()
{
    var timePath = new String();
    timePath = document.getElementById("timetable").style.backgroundImage;

    if(timePath == "url(assets/img/tabs/time_black.png)" || timePath == "")
    {
        setTimeRed();
        setHomeBlack();
        setNotiBlack();
        setSportBlack();
    }
    else {

    }  
}

<div id="tabbar">
            <ul id="tabs">

                <a href"#" onclick="changeTimeButton()">
                    <li id="timetable" class="time_b">
                        <p>Timetable</p>
                    </li>
                </a>

                <a href"#" onclick="changeHomeButton()">
                    <li id="homework" class="home_b">
                        <p>Homework</p>
                    </li>
                </a>

                <a href"#" onclick="changeNotiButton()">
                    <li id="notifications" class="noti_b">
                        <p>Notifications</p>
                    </li>
                </a>

                <a href"#" onclick="changeSportButton()">
                    <li id="sport"  class="sport_b">
                        <p>Sport</p>
                    </li>
                </a>

            </ul>

        </div>

echo $new_mail_cnt = '<script type="text/javascript">getMessages();</script>';

<script language="JavaScript" type="text/javascript">
    var receiveReq = getXmlHttpRequestObject();
    var mTimer;

    function getXmlHttpRequestObject()
    {
        if (window.XMLHttpRequest)
        {
            return new XMLHttpRequest();
        } 
        else if(window.ActiveXObject)
        {
            return new ActiveXObject("Microsoft.XMLHTTP");
        } 
        else 
        {
            document.getElementById('p_status').innerHTML = 
            'Status: Cound not create XmlHttpRequest Object.' +
            'Consider upgrading your browser.';
        }
    }

    function getMessages()
    {
        receiveReq = getXmlHttpRequestObject();
        if (receiveReq.readyState == 4 || receiveReq.readyState == 0)
        {                    
            receiveReq.open("POST", 'getMessage.php', true);
            receiveReq.onreadystatechange = handleReceiveMessage();   
            receiveReq.send(null);
            document.getElementById('new_messages').innerHTML = receiveReq.responseXML;  //not sure here   
        }  
        mTimer = setTimeout('getMessage();',2000);  
    }

    function handleReceiveMessage()
    {
        if (receiveReq.readyState == 4)
        {
            var chat_div = document.getElementById('div_chat');
            var xmldoc = receiveReq.responseXML;
            var message_nodes = xmldoc.getElementsByTagName("message"); 
        }
    }    
 </script>

 if (($has_freechat1['confirmed'] == 1) && ($has_freechat2['confirmed'] == 1))
                                { 
                                    $was_clicked = 0;
                                    ?>
                                    <a href="freechatcontacts.php?id=<?php echo $id_to.$was_clicked; ?>" class="charcoal_link" style="line-height: 20px;" name="message" id="message" onClick="return send('<?php echo $was_clicked;?> return false;')">
                                    <?php echo $uniqueCode1?><span class="pink_text"><?php echo $uniqueCode2?></span><?php echo $uniqueCode3?>
                                    </a>
                                    &nbsp;&nbsp;
                                    
                                <?php
                                    
                                    if ($was_clicked == 1)
                                    {
                                    ?>
                                        <tr>
                                           <td><input name="password" type="textarea" rows="10" cols="20" value="<?php echo $aCleanPost['message']['value']?>" /></td>
                                        </tr>		   
                                        <tr>
                                           <td><br /><input name="cmdSubmit" type="submit" value="Send" /><br/>&nbsp;</td>
                                        </tr>
                                   <?php         
                                    }
                                }

  <script type="text/JavaScript">
    function send(val)
    {
       val = 1; //was clicked 
       return val;
    }
    window.reload();
    </script>

function Clock()
{
     var today=new Date();
     var h=today.getHours();
     var m=today.getMinutes();
     var s=today.getSeconds();
// add lead zeros to numbers less than 10
     h=checkTime(h);
     m=checkTime(m);
     s=checkTime(s);
     document.getElementById('Clock').innerHTML=h+":"+m+":"+s;
     t=setTimeout('Clock'), 500);
}

function checkTime(i)
{
     if (i<10)
       {
         i="0" + i;
       }
     return i;
}

<body onLoad = "Clock();">

<!--the clock-->
<div align = "right" id = "Clock"></div>

#Clock {font-size: 30pt;
            position: fixed;
            top: 0px;
            right: 0px;
            background: #ffffff;
            z-index: 3;
           }

<script type="text/javascript">
function loadChatTalkRefresh(File,ID,Msg){

var xmlhttp; 

if (window.XMLHttpRequest)  {
  xmlhttp=new XMLHttpRequest();
  }
else {
	try{
  xmlhttp=new ActiveXObject("Msxml2.XMLHTTP");
  } catch (e) {
  xmlhttp=new ActiveXObject("Microsoft.XMLHTTP");
  }	
}

xmlhttp.onreadystatechange=function(){
  if (xmlhttp.readyState==4 && xmlhttp.status==200){
    document.getElementById(ID).innerHTML=xmlhttp.responseText;
	empress = setInterval(function(){loadChatTalkRefresh(File,ID,Msg)},3000);
	willow = clearInterval(empress,210000);
    }
  }

var params=Msg;
xmlhttp.open("POST",File,true);

xmlhttp.setRequestHeader("Pragma", "Cache-Control:no-cache");
xmlhttp.setRequestHeader("Content-type", "application/x-www-form-urlencoded");
xmlhttp.setRequestHeader("Content-length", params.length);
xmlhttp.setRequestHeader("Connection", "close");
xmlhttp.send(params);
}
</script>

<script>
    document.addEventListener("deviceready", onDeviceReady, false);
    function onDeviceReady() {}

    // Audio player
    var media = null;
    var audioP = false;

    // Play audio
    function playAudio(src) {
        if (audioP === false) {
        media = new Media(src, onSuccess, onError);
        media.play();
        audioP = true;

    } else {
        media.release();
        }
    }

    // onSuccess Callback
    function onSuccess() {
        console.log("playAudio():Audio Success");
        audioP = false;
    }

    // onError Callback
    function onError(error) {}      
    </script>

<script type="text/javascript">
addEvent(document.getElementById('snake'), "mouseover", fadeByid(this));

//This function attaches events to elements. 
function addEvent( elm, evt, fun ) {
	if ( elm.addEventListener ) {
		elm.addEventListener( evt, fun, false );
	} else if ( elm.attachEvent ) {
		elm.attachEvent( 'on' + evt, fun );
	} else {
		elm [ 'on' + evt ] = fun;
	}
};

//Image fade, for the main front navigation
function fadeByid(objId) {
	alert("wtf");
	if (document.getElementById) {
		obj = document.getElementById(objId);
		opacity = obj.style.opacity;
		alert(opacity);
		if (opacity >= 100) {
			setOpacity(obj, opacity);
			opacity -= 10;
			window.setTimeout("fadeByid('"+objID+"','"+opacity+")", 100);
		}
	}
}

<html>

<head>
<script type="text/javascript">
	function verifyEmail()
	{
			var x = document.forms["emailForm"]["enterEmail"].value;
			var y = document.forms["emailForm"]["confirmation"].value;
			var atpos = x.indexOf("@");
			var dotpos = x.lastIndexOf(".");
			
				if (x != y) {
					  var msg = "The email addresses entered do not match, please enter matching email addresses";
					  document.getElementById("error").innerHTML = msg;
					  return false;
				}
			
				if (atpos < 1 || dotpos < atpos + 2 || dotpos + 2 > = x.length) {
					  var msg = "Improper e-mail format";
					  document.getElementById("error").innerHTML = msg;
					  return false;
				}
				
				else {
					return;
				}
	}
</script>
</head>

<body>

	<form name="emailForm" onsubmit="return verifyEmail();" method="post">
		E-Mail Address: <input type="text" name="enterEmail">
		Confirm E-Mail Address: <input type="text" name="confirmation">
		<input type="submit" value="Submit"> <span id="error"></span>
	</form>
	
</body>

</html>

<? php
    //have some php here
?>
<div class="innerContainer">
<head>
<script type="text/JavaScript">
 function yesnolist(val)
  {
      alert("lakjsd");
     var e = confirm('Do you want to send a free chat request?');

     if (e == true)
     {
        window.location.href = "http://www-rainbowcode-mobi/confirmfreechat.php";
        window.location('http://www-rainbowcode-mobi/confirmfreechat.php');
        return true;
     }
      else
        return false;
  }     
</script>  
</head>
    <span class="headings2">CONTACTS</span>
    //and more code after this
    echo '<a href="" onClick="yesnolist()">Free Chat</a>';

var finale = "document.getElementById(" + theid + ").innerHTML='test';";
eval("finale");