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deleting break tags after refreshing

I having problem with the refresh of a topic when there is a block of code in it.
If i post some comment in a topic and i use break tags to get white space between the lines, everything is ok.
When i put some code in it with the pre tags under the last plaint text with some breaks, everything looks oke also.
The problem occurs when refreshing the page; geshi is being parsed and he destroys the break tags between the last plain text and the code block.
How can i resolve this problem? Why is this happening?

See images below:

Image 1: after submit but before refresh:

Image 2: after submit and after refresh:

This is the piece of code of geshi with the rel atttribute i added to it ( but i don't think it has to do something with this)

function ParseSyntax($String) {
    $String = preg_replace_callback("/\s*<pre(?:lang=[\"']([\w-]+)[\"']|line=[\"'](\d*)[\"']|escaped=[\"'](true|false)?[\"']|\s)+>(.*)<\/pre>\s*/siU",'pre_entities', $String);
    return $String;

function pre_entities($match) {
    $language = strtolower(trim($match[1]));
    $line = trim($match[2]);
    $escaped = trim($match[3]);
    $code = geshisyntax_code_trim($match[4]);
    if ($escaped == "true") $code = htmlspecialchars_decode($code);

    $geshi = new GeSHi($code, $language);
    echo '<style type="text/css">'.$geshi->get_stylesheet()."</style>";

    $element_id = uniqid(); //generate unique ID
    $output = '';
    $output .='<a rel="highlight'.$element_id.'" class="selectable">[Selecteer Code]</a>'; // assign unique ID to rel attribute

        $output .= "<div class='geshi_syntax'><table><tr>";

    if ($line) {

    $output .= "<td class='line_numbers'>";
    $output .= geshisyntax_line_numbers($code, $line);
    $output .= '</td><td class="code">';

    $output .= '<div id="highlight'.$element_id.'" class="code">'; // assign unique ID to div

    $output .= $geshi->parse_code();
    $output .= '</div>';
    $output .= "</td>";

    else {
        $output .= "<td>";
        $output .= '<div id="highlight'.$element_id.'" class="code">'; // assign unique ID to div
        $output .= $geshi->parse_code();
        $output .= "</div>";
        $output .= "</td>";


    $output .= "</tr></table></div>";

   return $output;


function geshisyntax_line_numbers($code, $start) {
    $line_count = count(explode("\n", $code));
    $output = "<pre>";
    for ($i = 0; $i < $line_count; $i++)
        $output .= ($start + $i) . "\n";
    $output .= "</pre>";
    return $output;

function geshisyntax_code_trim($code) {
    // special ltrim b/c leading whitespace matters on 1st line of content
    $code = preg_replace("/^\s*\n/siU", "", $code);
    $code = rtrim($code);
    return $code;


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