hi,
in this code "Virtual Directories" and "Files" are sort alphabetically, but i don't know how to sort "Non Virtual Directories" ???
Thanks for your help and sorry for my bad english !

	// For Virtual Directories
	if($path == '' || $path == '/'){

		$query = sprintf('select * from %spermissions inner join %sbins on %spermissions.binid=%sbins.id where userid="%s" and %sbins.name ="%s" order by display',
						$GLOBALS['tablePrefix'],
						$GLOBALS['tablePrefix'],
						$GLOBALS['tablePrefix'],
						$GLOBALS['tablePrefix'],
						$_SESSION['userid'],
						$GLOBALS['tablePrefix'],
						$_SESSION['user']);
						
		$result = mysql_query($query,$database) or die( error('Get Folder query failed') );
		
		while($bins = mysql_fetch_assoc($result)) {
			$listing[] = array(  displayname => $bins['display'],
										scheme => $bins['scheme'],
										type => "directory",
										name => $bins['name'],
										path => '/'. $bins['name'],
										virtual => "true" );
		}				
			
		$query = sprintf('select * from %spermissions inner join %sbins on %spermissions.binid=%sbins.id where userid="%s" and %sbins.name !="%s" order by display',
						$GLOBALS['tablePrefix'],
						$GLOBALS['tablePrefix'],
						$GLOBALS['tablePrefix'],
						$GLOBALS['tablePrefix'],
						$_SESSION['userid'],
						$GLOBALS['tablePrefix'],
						$_SESSION['user']);
						
		$result = mysql_query($query, $database) or die( error('Get Folder query failed') );
		$vdcount = mysql_num_rows($result);
		
		switch(true) {
			case ($vdcount >= 1):
				$virtual = "closed";
				break;
			case ($vdcount == 1):
				$virtual = "true";
				break;
			default :
				$virtual = "false";
		}
		
		if($vdcount > 0)
			while($bins = mysql_fetch_assoc($result)){
				$listing[] = array(  displayname => $bins['display'],
											scheme => $bins['scheme'],
											type => "directory",
											name => $bins['name'],
											path => '/'. $bins['name'],
											virtual => $virtual );
			}
			
		echo $json->encode($listing);
		exit;
	}


	// Non Virtual Directories
	if( getUserAuth('view', $path) ){
		logAction('list',$path);
		$fullpath = getUserPath($path).$path;
		databaseSync($fullpath,$path);
		
		// Directories
		if (is_dir($fullpath)) {
			if ($dh = opendir($fullpath)) {
			   while (($file = readdir($dh)) !== false) {
			     if(substr($file,0,1) != '.' && is_dir($fullpath . '/' . $file)) {
						$listing[] = array( 
									type => "directory", 
									name => $file, 
									path => $path .'/'. $file );
				  }
			   }
			   closedir($dh);
			}
		}
		else error("directory doesnt exist $fullpath");

		// Files
		$query = sprintf('select *,date_format(`date`,"%s") as `dateformatted` from %sfilesystem where path="%s" and status="%s" order by `filename',
								$dateFormat,
								$GLOBALS['tablePrefix'],
								$fullpath,
								"found" );
								
		$result = mysql_query($query,$database) or die( error('Get Folder query failed') );
		while($files = mysql_fetch_assoc($result)) {
			$listing[] = array(	type => "file",
										name => $files['filename'],
										date => $files['dateformatted'],
										id => $files['id'] );
		}
	      
	}
	else error("Access Denied $path");
	
	echo $json->encode($listing);
	exit;
}

Perhaps, asort() - http://www.php.net/manual/en/function.asort.php

It's hard to define your situation because of your image is too litle.
By the way, the order of folders is depends from OS settings.