I use a php file to generate a javascript array, so when i include it in the file it executes the javascript ok! But when i try and use jquery to reload the file after a minute it doesn't work and won't execute the javascript any ideas on a similar idea or fix?

Using PHP has no bearing on how or why JavaScript executes, so forget that part of the question. All that is left, is what does the client-side code look like (what is output to the browser)?

PHP Code:

<?php 
    include("config.php");

$pagePost = 1;
$match = mysql_fetch_array(mysql_query("SELECT * FROM `manager__fixtures` WHERE `id` = '" . $pagePost . "'"));
$information = array();
// Time
$time = $match['kick_off'];
$match_time = (($match['day'] * 86400) + $_SESSION['season_start']);
$output = strtotime(date("dS F Y $time", $match_time)) + 5400;
if(time() > $output)
{
$information["minute"] = "| <strong>R</strong>";
} else {
$information["minute"] = "| <strong>" . (90 - floor(($output - time()) / 60)) . " min</strong>";
} 
if(time() > $output) 
{
$min = 90;
} else {
$min = (90 - floor(($output - time()) / 60));
}

//Score
$home_score = mysql_num_rows(mysql_query("SELECT * FROM `manager__shots` WHERE `match_id` = '" . $pagePost . "' && `type` = 'Goal' && `team_id` = '" . $match['home_team'] . "' && `min` <= '" . $min . "'"));

$away_score = mysql_num_rows(mysql_query("SELECT * FROM `manager__shots` WHERE `match_id` = '" . $pagePost . "' && `type` = 'Goal' && `team_id` = '" . $match['away_team'] . "' && `min` <= '" . $min . "'"));
//$information["score"] = "<strong style=\'font-size: 120%;\'>" . $home_score . " - " . $away_score . "</strong>";

$information['minute'] = date("s", time());


//Convert PHP Array To Javascript Array
        function get_javascript_array($phpArray, $jsArrayName, &$html = '') {
                $html .= $jsArrayName . " = new Array(); \r\n ";
                foreach ($phpArray as $key => $value) {
                        $outKey = (is_int($key)) ? '[' . $key . ']' : "['" . $key . "']";

                        if (is_array($value)) {
                                get_javascript_array($value, $jsArrayName . $outKey, $html);
                                continue;
                        }
                        $html .= $jsArrayName . $outKey . " = ";
                        if (is_string($value)) {
                                $html .= "'" . $value . "'; \r\n ";
                        } else if ($value === false) {
                                $html .= "false; \r\n";
                        } else if ($value === NULL) {
                                $html .= "null; \r\n";
                        } else if ($value === true) {
                                $html .= "true; \r\n";
                        } else {
                                $html .= $value . "; \r\n";
                        }
                }
               
                return $html;
        }
//Return The Match Information
    ?>
    <script>
    <?php echo get_javascript_array($information, "information"); ?>
    $("#time").html(information['minute']);
    </script>

And The Output Which Doesn't update the time div!

<script>
    information = new Array(); 
 information['minute'] = '29'; 
     $("#time").html(information['minute']);
    </script>

That's not what is being outputted to the browser, it is just an extra puzzle to solve with all that PHP in there. You said the PHP output part is ok. Either a link to the actual page or a copy-paste of the important part of the "view source" is what is needed.

http://www.championshipfl.com/

then click on match report in the middle!

When it first loads it is ok and will get the data but i want to refresh it after every minute to get new content but it just doesn't rexecute the javascript outputted.

ive found the solution! it returns the array so i used eval() and now i can call upon the new array values!