I have shell access to the server(s) as they are mine.
drwxr-xr-x 2 joomla nogroup 4096 Jan 18 19:20 logs
lrwxrwxrwx 1 joomla 37862 35 Jan 18 19:20 administrator -> /www/home/joomlaPrime/administrator
lrwxrwxrwx 1 joomla 37862 32 Jan 18 19:20 components -> /www/home/joomlaPrime/components
lrwxrwxrwx 1 joomla 37862 30 Jan 18 19:20 includes -> /www/home/joomlaPrime/includes
lrwxrwxrwx 1 joomla 37862 30 Jan 18 19:20 language -> /www/home/joomlaPrime/language
lrwxrwxrwx 1 joomla 37862 31 Jan 18 19:20 libraries -> /www/home/joomlaPrime/libraries
lrwxrwxrwx 1 joomla 37862 27 Jan 18 19:20 media -> /www/home/joomlaPrime/media
lrwxrwxrwx 1 joomla 37862 29 Jan 18 19:20 modules -> /www/home/joomlaPrime/modules
lrwxrwxrwx 1 joomla 37862 29 Jan 18 19:20 plugins -> /www/home/joomlaPrime/plugins
lrwxrwxrwx 1 joomla 37862 28 Jan 18 19:20 xmlrpc -> /www/home/joomlaPrime/xmlrpc
lrwxrwxrwx 1 joomla 37862 31 Jan 18 19:20 .htaccess -> /www/home/joomlaPrime/.htaccess
lrwxrwxrwx 1 joomla 37862 32 Jan 18 19:20 robots.txt -> /www/home/joomlaPrime/robots.txt
-rwxr-xr-x 1 joomla nogroup 1865 Jan 18 19:21 config_multisites.php
-rwxr-xr-x 1 joomla nogroup 444 Jan 18 19:21 index.php
-rwxr-xr-x 1 joomla nogroup 446 Jan 18 19:21 index2.php
drwxr-xr-x 8 joomla nogroup 4096 Jan 24 11:40 cache
drwxr-xr-x 6 joomla nogroup 4096 Jan 24 12:37 templates
-r--r--r-- 1 joomla nogroup 1808 Jan 24 12:39 configuration.php
drwxr-xr-x 3 joomla nogroup 4096 Jan 26 13:19 tmp
drwxr-xr-x 8 joomla nogroup 4096 Jan 26 15:24 images
drwxr-xr-x 13 joomla nogroup 4096 Jan 27 13:17 ..
drwxr-xr-x 8 joomla nogroup 4096 Jan 27 13:50 .
Seems fine to me. I assume your JCKEditor works fine on your sites? Maybe you can show me what your config files are in a PM as far as how JCK has them in the module config.