Well, if anyone else was wondering, I figured it out. Looks like the problem was in the array_search() that was checking for the extension being listed in the $enabledextension array. I changed it up to be a strstr() encapsulated in a foreach() that runs through the array and fixed it. Here is the correct code for the PanelReOrder function:

function PanelReOrder(&$Context) {
$this->Name = 'PanelReOrder';
$this->ValidActions = array('PanelReOrder');
$this->Constructor($Context);

if ($this->IsPostBack) {
$Context->PageTitle = $this->Context->GetDefinition('PanelReOrder');

if ($this->PostBackAction == 'PanelReOrder') {
// Add the javascript to the head for sorting categories
global $Head;
$Head->AddScript('js/prototype.js');
$Head->AddScript('js/scriptaculous.js');

if (!file_exists($Context->Configuration['EXTENSIONS_PATH'].'PanelOrder/panelextensions.ini')) {
$panelextensions = fopen($Context->Configuration['EXTENSIONS_PATH'].'PanelOrder/panelextensions.ini','w+');
fwrite($panelextensions,"[PanelOrder]\r\n");
} else {
$panelextensions = fopen($Context->Configuration['EXTENSIONS_PATH'].'PanelOrder/panelextensions.ini','a');
}

$enabledextensions = file($Context->Configuration['APPLICATION_PATH'].'/conf/extensions.php');
foreach ($enabledextensions as $ext_num => $currentextension) {
if (strstr($currentextension, "include")) {
$panelarray = parse_ini_file($Context->Configuration['EXTENSIONS_PATH'].'PanelOrder/panelextensions.ini');
$panelnumber = count($panelarray);
$currentextensionarray = explode('"', $currentextension);
$extensionfile = $currentextensionarray[1];
if ($extensionfile != "PanelOrder/default.php") {
$fullextensionpath = $Context->Configuration['EXTENSIONS_PATH'].$extensionfile;
if (!is_int(array_search($fullextensionpath, $panelarray))) {
$currentextensioncontents = file($fullextensionpath);
foreach ($currentextensioncontents as $line_num => $line) {
if (strstr($line,"\$Panel->AddString(") || strstr($line,"\$Panel->AddList(")) {
fwrite($panelextensions,$panelnumber."=".$fullextensionpath."\r\n");
break;
}
}
}
}
}
}
fclose($panelextensions);

$panelarray = parse_ini_file($Context->Configuration['EXTENSIONS_PATH'].'PanelOrder/panelextensions.ini');
$panelnumber = count($panelarray);
$neworder = "[PanelOrder]\r\n";
$n = 0;
for ($i = 0;$i < $panelnumber;$i++) {
$found = false;
$x = $i - $n;
$explode = explode($Context->Configuration['EXTENSIONS_PATH'],$panelarray[$i]);
$search = 'include($Configuration[\'EXTENSIONS_PATH\']."'.$explode[1].'");'."\r\n";
foreach($enabledextensions as $anext) {
if(strstr($anext,$explode[1])) {
$found = true;
}
}
if ($found) {

$neworder .= $x."=".$panelarray[$i]."\r\n";
} else {
$n++;
}
}
$rewritefile = fopen($Context->Configuration['EXTENSIONS_PATH'].'PanelOrder/panelextensions.ini', 'w+');
fwrite($rewritefile,$neworder);
fclose($rewritefile);

}
}
}

Okay, I just tried this using the below code, (which may or may not be the same as you posted :P) and it doesn't seem to be working for me with or without the JQuery and Set List extensions enabled or disabled.

I can drag the boxes around just fine, and they remember where they were put, but it still just seems to keep my extension options in alphabetical order.

Lines 65-74

				for ($i = 0;$i < $panelnumber;$i++) {
					$found = false;
					$x = $i - $n;
					$explode = explode($Context->Configuration['EXTENSIONS_PATH'],$panelarray[$i]);
					$search = 'include($Configuration[\'EXTENSIONS_PATH\']."'.$explode[1].'");'."\r\n";
					foreach($enabledextensions as $anext) {
						if(strstr($anext,$explode[1])) {
							$found = true;
						}
					}
					if ($found) {

						$neworder .= $x."=".$panelarray[$i]."\r\n";
					} else {
						$n++;
					}
				}