permission error

You should contact your system administrator that caused that things stopped working
Theoretically he could also change the user that is running apache - it may be no longer "apache", it depends on the server configuration.

The easiest way to check whether the permissions are ok, would be to launch a simple PHP script that tries to create a new empty file:

<?php

// Enable error reporting to see what's going on.
error_reporting(E_ALL);
ini_set('display_errors', 1);

// Put here a path to a file inside of the folder 
// where CKFinder should store uploaded files.

touch( "file.txt" );