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It wasn't just about the variable but the location of the IF loop. 

 

$subscriptionLevels = array(
    's2member_level3' => 'Yearly',
    's2member_level2' => 'Semi-annual',
    's2member_level1' => 'Monthly'
);

$query = 'SELECT um1.meta_value as custom, um2.meta_value as level, u.ID,u.user_login, u.user_email
           FROM wp_usermeta um1 
           INNER JOIN wp_usermeta um2
             ON um1.user_id = um2.user_id
           JOIN wp_users u
             ON um1.user_id = u.ID
           WHERE um1.meta_key = "wp_s2member_custom_fields"
             AND um2.meta_value LIKE "%s2member_level%"
		 GROUP BY um1.user_id';

$result = mysql_query($query);

//Process results into temp array
$regionData = array();
while($row = mysql_fetch_assoc($result))
{    
    //var_dump($row);

    $custom = unserialize($row['custom']);
    $user_region = $custom['county'];
    $level = unserialize($row['level']);
    $level_desc = key($level); //E.g. s2member_level3

if ($level_desc != "s2member_level4") {	
    $user_level = $subscriptionLevels[$level_desc];
}

    if(!isset($regionData[$user_region]))
    {
        $regionData[$user_region] = array_fill_keys($subscriptionLevels, 0);
    }
    $regionData[$user_region][$user_level]++;
}

//Output the results

foreach ($regionData as $region => $data)
{if ($region != 0) {
    echo "<br>Region {$region}<br>\n";

    foreach($data as $subscription_type => $member_count)	
    {

var_dump($subscription_type);
        echo "{$subscription_type}: {$member_count} members<br>\n";
}

}
}

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