<?PHP
if(!isset($_COOKIE['oauth_token'])){
session_start();
if (empty($_SESSION['access_token']) || empty($_SESSION['access_token']['oauth_token']) || empty($_SESSION['access_token']['oauth_token_secret'])) {header('Location: ./clearsessions.php');}

$access_token = $_SESSION['access_token'];
$connection = new TwitterOAuth(CONSUMER_KEY, CONSUMER_SECRET, $access_token['oauth_token'], $access_token['oauth_token_secret']);

setcookie('oauth_token', $access_token['oauth_token'], time()+60*60*24*30);
setcookie('oauth_token_secret', $access_token['oauth_token_secret'], time()+60*60*24*30);
}
//else use the cookies
else{
$oauth_token = $_COOKIE['oauth_token'];
$oauth_token_secret = $_COOKIE['oauth_token_secret'];
$connection = new TwitterOAuth(CONSUMER_KEY, CONSUMER_SECRET, $oauth_token, $oauth_token_secret);
}
?>

Does not work with the rest of my code, yet this does;

<?PHP
session_start();
if (empty($_SESSION['access_token']) || empty($_SESSION['access_token']['oauth_token']) || empty($_SESSION['access_token']['oauth_token_secret'])) {header('Location: ./clearsessions.php');}

$access_token = $_SESSION['access_token'];
$connection = new TwitterOAuth(CONSUMER_KEY, CONSUMER_SECRET, $access_token['oauth_token'], $access_token['oauth_token_secret']);
?>

Which is just a direct snippet from the larger cookie piece of code.

From what I can tell it's not using the stored cookies either (but that could be for other reasons) which means there must be a problem with this snippet and the larger piece of code, which I have included below. 

<?php
require_once('twitteroauth/twitteroauth.php');require_once('config.php');

//database connection.

if(!isset($_COOKIE['oauth_token'])){
session_start();
if (empty($_SESSION['access_token']) || empty($_SESSION['access_token']['oauth_token']) || empty($_SESSION['access_token']['oauth_token_secret'])) {header('Location: ./clearsessions.php');}

$access_token = $_SESSION['access_token'];
$connection = new TwitterOAuth(CONSUMER_KEY, CONSUMER_SECRET, $access_token['oauth_token'], $access_token['oauth_token_secret']);

setcookie('oauth_token', $access_token['oauth_token'], time()+60*60*24*30);
setcookie('oauth_token_secret', $access_token['oauth_token_secret'], time()+60*60*24*30);
}
//else use the cookies
else{
$oauth_token = $_COOKIE['oauth_token'];
$oauth_token_secret = $_COOKIE['oauth_token_secret'];
$connection = new TwitterOAuth(CONSUMER_KEY, CONSUMER_SECRET, $oauth_token, $oauth_token_secret);
}

$apistatus = $connection->get('account/rate_limit_status');
$remaininghits = $apistatus->remaining_hits;
if($remaininghits >= 50){

$param = array('count' => 1);
$mostrecenttweet = $connection->get('statuses/user_timeline', $param);
$userinfo = $connection->get('account/verify_credentials');

$uid = $userinfo->id;
$uname = $userinfo->screen_name;
$tweetcount = $userinfo->statuses_count;
$resettime = $apistatus->reset_time;
$mostrecentid = $mostrecenttweet[0]->id_str;

$SQL = "SELECT uid FROM users WHERE uid = '$uid'";
$result = mysql_query($SQL);

if(mysql_num_rows($result) == false){
$debug = 'first entry';

$store = "INSERT INTO users (uid, uname, tweetcount, mostrecentid, count, debug) VALUES ('$uid', '$uname', '$tweetcount', '$mostrecentid', 1, '$debug')";
mysql_query($store);
$id = md5('=a!-nd'.$uid);
$store = "INSERT INTO notes (id, uid, tid, note, hidden) VALUES ('$id', '$uid', '0', 'Your very first note, welcome!', 0)";
mysql_query($store);

for($page = 1; $page <= 16; ++$page){
$params = array('page' => $page, 'count' => 200);
$content = $connection->get('statuses/user_timeline', $params);
foreach($content as $post){
$ctid = $post->id_str;
$id = md5('=a!-nd'.$ctid);
if(preg_match('(^(Note to self|NTS)\W*|#NTS$)', $post->text)){
$title = preg_replace('(^(Note to self|NTS)\W*|#NTS$)', '', $post->text);
$store = "INSERT INTO notes (id, uid, tid, note, hidden) VALUES ('$id', '$uid', '$ctid', '$title', 0)";mysql_query($store);}
}}
}

else{
$debug = 'already registered';

$sql = "SELECT mostrecentid, count, tweetcount FROM users WHERE uid = '$uid'";
$queryresult = mysql_query($sql);
$result = mysql_fetch_array($queryresult);
$currentcount = $result['count'] + 1;
$ltid = $result['mostrecentid'];
$tweetcountold = $result['tweetcount'];
$tweetsbetween = $tweetcount - $tweetcountold;
$pageno = ceil($tweetsbetween / 200);

for($page = 1; $page <= $pageno; ++$page){
$params = array('since_id' => $ltid, 'page' => $page);
$content = $connection->get('statuses/user_timeline', $params);
foreach($content as $post){
$ctid = $post->id_str;
$id = md5('=a!-nd'.$ctid);
$SQL = "SELECT uid, tid FROM notes WHERE uid = '$uid' AND tid = '$ctid'";
$result = mysql_query($SQL);
if(mysql_num_rows($result) == false){
if(preg_match('(^(Note to self|NTS)\W*|#NTS$)', $post->text)){
	$title = preg_replace('(^(Note to self|NTS)\W*|#NTS$)', '', $post->text);
	$store = "INSERT INTO notes (id, uid, tid, note, hidden) VALUES ('$id', '$uid', '$ctid', '$title', 0)";
	mysql_query($store);
}}}}

$updateuser = "UPDATE users SET tweetcount = '$tweetcount', uname = '$uname', mostrecentid = '$mostrecentid', count = '$currentcount', debug = '$debug' WHERE uid = '$uid'";
mysql_query($updateuser);
}

$notes = array();
$SQL = "SELECT id, note FROM notes WHERE uid = '$uid' AND hidden = 0 ORDER BY tid ASC";
	$results = mysql_query($SQL);	
	while($rows = mysql_fetch_array($results)){
	$notes[] = $rows['note'].'<a style="float:right;" href="http://lewisjuggins.co.uk/oauth/delete.php?id='.$rows['id'].'">&#10003;</a><br/><br/>';
	}


$notesdone = array();
$SQL = "SELECT id, note FROM notes WHERE uid = '$uid' AND hidden = 1 ORDER BY tid DESC LIMIT 0, 5 ";
	$results = mysql_query($SQL);	
	while($rows = mysql_fetch_array($results)){
	$notesdone[] = $rows['note'].'<br/><br/>';
	}
}



else{
$notes = 'You dont have enough API calls to use this, please wait for your reset at '.$resettime;
}

mysql_close($db_handle);

/* Include HTML to display on the page. */
include('html.inc');
?>