I had a problem like this earlier today, and I found that the manifest.xml file had some code misplaced or so I believe.
<hook id="ft_about_pre_copyright"><![CDATA[
if (defined('PUN_BBCODE_BAR_INCLUDE')) {
include $ext_info['path'].'/bar.php';
?>
<script type="text/javascript"><!--
var pun_bbcode_bar = document.getElementById("pun_bbcode_bar");
if (pun_bbcode_bar) {
pun_bbcode_bar.innerHTML = "<?php echo pun_bbcode_bar(); ?>";
pun_bbcode_bar.style.display = "block";
pun_bbcode_bar.style.visibility = "visible";
}
--></script>
<?php
}
]]></hook>
I placed the piece of code inside that hook here.
<hook id="po_pre_post_contents, vt_quickpost_pre_message_box, ed_pre_message_box, pun_pm_fn_send_form_pre_textarea_output"><![CDATA[
if ($forum_user['pun_bbcode_enabled']) {
define('PUN_BBCODE_BAR_INCLUDE', 1);
echo "\t\t\t".'<div class="sf-set" id="pun_bbcode_bar"></div>'."\n";
}
if (defined('PUN_BBCODE_BAR_INCLUDE')) {
include $ext_info['path'].'/bar.php';
?>
<script type="text/javascript"><!--
var pun_bbcode_bar = document.getElementById("pun_bbcode_bar");
if (pun_bbcode_bar) {
pun_bbcode_bar.innerHTML = "<?php echo pun_bbcode_bar(); ?>";
pun_bbcode_bar.style.display = "block";
pun_bbcode_bar.style.visibility = "visible";
}
--></script>
<?php
}
]]></hook>
So the final result looked like this
<hook id="po_pre_post_contents, vt_quickpost_pre_message_box, ed_pre_message_box, pun_pm_fn_send_form_pre_textarea_output"><![CDATA[
if ($forum_user['pun_bbcode_enabled']) {
define('PUN_BBCODE_BAR_INCLUDE', 1);
echo "\t\t\t".'<div class="sf-set" id="pun_bbcode_bar"></div>'."\n";
}
if (defined('PUN_BBCODE_BAR_INCLUDE')) {
include $ext_info['path'].'/bar.php';
?>
<script type="text/javascript"><!--
var pun_bbcode_bar = document.getElementById("pun_bbcode_bar");
if (pun_bbcode_bar) {
pun_bbcode_bar.innerHTML = "<?php echo pun_bbcode_bar(); ?>";
pun_bbcode_bar.style.display = "block";
pun_bbcode_bar.style.visibility = "visible";
}
--></script>
<?php
}
]]></hook>
<hook id="ft_about_pre_copyright"><![CDATA[
]]></hook>
I think this might just be some funky glitch with my installment of punbb, but you could give it a try yourself since it did seem to solve the problem.