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And yes I have properly chmoded all directories
My base folder displays the following permissions
drwxr-xr-x.  7 apache apache   4096 Mar 25 20:05 admin
-rw-r--r--.  1 apache apache   3581 Mar 21 17:00 announcements.php
drwxr-xr-x.  2 apache apache   4096 Mar 25 20:05 archive
-rw-r--r--.  1 apache apache   4669 Mar 21 17:00 attachment.php
drwxrwxrwx.  3 apache apache   4096 Mar 25 20:05 cache
-rw-r--r--.  1 apache apache  75371 Mar 21 17:00 calendar.php
-rw-r--r--.  1 apache apache   7644 Mar 21 17:00 captcha.php
-rw-r--r--.  1 apache apache   8356 Mar 21 17:00 contact.php
-rw-r--r--.  1 apache apache    850 Mar 21 17:00 css.php
-rw-r--r--.  1 apache apache  28756 Mar 21 17:00 editpost.php
-rw-r--r--.  1 apache apache  40565 Mar 21 17:00 forumdisplay.php
-rw-r--r--.  1 apache apache  31843 Mar 25 20:04 global.php
-rw-r--r--.  1 apache apache   1583 Mar 21 17:00 htaccess-nginx.txt
-rw-r--r--.  1 apache apache   2753 Mar 21 17:00 htaccess.txt
drwxr-xr-x.  7 apache apache   4096 Mar 25 20:05 images
drwxr-xr-x. 10 apache apache   4096 Jun 17 20:20 inc
-rw-r--r--.  1 apache apache  11032 Mar 21 17:00 index.php
drwxr-xr-x.  4 apache apache   4096 Mar 25 20:05 install
drwxr-xr-x.  6 apache apache   4096 Mar 25 20:05 jscripts
-rw-r--r--.  1 apache apache  12239 Mar 21 17:00 managegroup.php
-rw-r--r--.  1 apache apache  11637 Mar 21 17:00 memberlist.php
-rw-r--r--.  1 apache apache  94366 Mar 21 17:00 member.php
-rw-r--r--.  1 apache apache  29051 Mar 21 17:00 misc.php
-rw-r--r--.  1 apache apache 137958 Mar 21 17:00 modcp.php
-rw-r--r--.  1 apache apache  90134 Mar 21 17:00 moderation.php
-rw-r--r--.  1 apache apache  45201 Mar 21 17:00 newreply.php
-rw-r--r--.  1 apache apache  35676 Mar 21 17:00 newthread.php
-rw-r--r--.  1 apache apache   7261 Mar 21 17:00 online.php
-rw-r--r--.  1 apache apache  28294 Mar 21 17:00 polls.php
-rw-r--r--.  1 apache apache  21981 Mar 21 17:00 portal.php
-rw-r--r--.  1 apache apache   6636 Mar 21 17:00 printthread.php
-rw-r--r--.  1 apache apache  67938 Mar 21 17:00 private.php
-rw-r--r--.  1 apache apache   4080 Mar 21 17:00 ratethread.php
-rw-r--r--.  1 apache apache   5512 Mar 21 17:00 report.php
-rw-r--r--.  1 apache apache  33254 Mar 21 17:00 reputation.php
-rw-r--r--.  1 apache apache    423 Mar 21 17:00 rss.php
-rw-r--r--.  1 apache apache  48478 Mar 25 20:04 search.php
-rw-r--r--.  1 apache apache   7915 Mar 21 17:00 sendthread.php
-rw-r--r--.  1 apache apache   5287 Mar 21 17:00 showteam.php
-rw-r--r--.  1 apache apache  49650 Mar 21 17:00 showthread.php
-rw-r--r--.  1 apache apache   6122 Mar 21 17:00 stats.php
-rw-r--r--.  1 apache apache   6528 Mar 21 17:00 syndication.php
-rw-r--r--.  1 apache apache   1685 Mar 21 17:00 task.php
drwxrwxrwx.  3 apache apache   4096 Jun 17 20:27 uploads
-rw-r--r--.  1 apache apache   7031 Mar 21 17:00 usercp2.php
-rw-r--r--.  1 apache apache 121888 Mar 25 20:04 usercp.php
-rw-r--r--.  1 apache apache  23764 Mar 21 17:00 warnings.php
-rw-r--r--.  1 apache apache  30691 Mar 21 17:00 xmlhttp.php
The inc folder has the following

drwxr-xr-x. 5 apache apache   4096 Mar 25 20:05 3rdparty
-rw-r--r--. 1 apache apache   3285 Mar 21 17:00 adminfunctions_templates.php
drwxr-xr-x. 2 apache apache   4096 Mar 25 20:05 cachehandlers
drwxr-xr-x. 2 apache apache   4096 Mar 25 20:05 captcha_fonts
-rw-r--r--. 1 apache apache  10689 Mar 21 17:00 class_captcha.php
-rw-r--r--. 1 apache apache  13980 Mar 21 17:00 class_core.php
-rw-r--r--. 1 apache apache  14233 Mar 21 17:00 class_custommoderation.php
-rw-r--r--. 1 apache apache  29140 Mar 21 17:00 class_datacache.php
-rw-r--r--. 1 apache apache  17734 Mar 21 17:00 class_error.php
-rw-r--r--. 1 apache apache   6725 Mar 21 17:00 class_feedgeneration.php
-rw-r--r--. 1 apache apache   5964 Mar 21 17:00 class_feedparser.php
-rw-r--r--. 1 apache apache   8466 Mar 21 17:00 class_graph.php
-rw-r--r--. 1 apache apache   5073 Mar 21 17:00 class_language.php
-rw-r--r--. 1 apache apache   9727 Mar 25 20:04 class_mailhandler.php
-rw-r--r--. 1 apache apache 102511 Mar 21 17:00 class_moderation.php
-rw-r--r--. 1 apache apache  45282 Mar 25 20:04 class_parser.php
-rw-r--r--. 1 apache apache   5841 Mar 21 17:00 class_plugins.php
-rw-r--r--. 1 apache apache  15346 Mar 21 17:00 class_session.php
-rw-r--r--. 1 apache apache   5769 Mar 21 17:00 class_stopforumspamchecker.php
-rw-r--r--. 1 apache apache   3959 Mar 21 17:00 class_templates.php
-rw-r--r--. 1 apache apache   2018 Mar 21 17:00 class_timers.php
-rw-r--r--. 1 apache apache   3562 Mar 21 17:00 class_xml.php
-rwxrwxrwx. 1 apache apache      0 Mar 21 17:00 config.php
-rw-r--r--. 1 apache apache   4209 Mar 21 17:00 datahandler.php
drwxr-xr-x. 2 apache apache   4096 Mar 25 20:05 datahandlers
-rw-r--r--. 1 apache apache  12300 Mar 21 17:00 db_base.php
-rw-r--r--. 1 apache apache  36494 Mar 21 17:00 db_mysqli.php
-rw-r--r--. 1 apache apache  36485 Mar 21 17:00 db_mysql.php
-rw-r--r--. 1 apache apache   5000 Mar 21 17:00 db_pdo.php
-rw-r--r--. 1 apache apache  37978 Mar 21 17:00 db_pgsql.php
-rw-r--r--. 1 apache apache  36790 Mar 21 17:00 db_sqlite.php
-rw-r--r--. 1 apache apache   6051 Mar 21 17:00 functions_archive.php
-rw-r--r--. 1 apache apache  26704 Mar 21 17:00 functions_calendar.php
-rw-r--r--. 1 apache apache  18580 Mar 21 17:00 functions_forumlist.php
-rw-r--r--. 1 apache apache   6266 Mar 21 17:00 functions_image.php
-rw-r--r--. 1 apache apache   8231 Mar 21 17:00 functions_indicators.php
-rw-r--r--. 1 apache apache   5681 Mar 21 17:00 functions_massmail.php
-rw-r--r--. 1 apache apache   8668 Mar 21 17:00 functions_modcp.php
-rw-r--r--. 1 apache apache  32780 Mar 21 17:00 functions_online.php
-rw-r--r--. 1 apache apache 198452 Mar 11 17:43 functions.php
-rw-r--r--. 1 apache apache   6456 Mar 21 17:00 functions_posting.php
-rw-r--r--. 1 apache apache  30713 Mar 21 17:00 functions_post.php
-rw-r--r--. 1 apache apache   4496 Mar 21 17:00 functions_rebuild.php
-rw-r--r--. 1 apache apache  45015 Mar 21 17:00 functions_search.php
-rw-r--r--. 1 apache apache   8960 Mar 21 17:00 functions_serverstats.php
-rw-r--r--. 1 apache apache   9205 Mar 21 17:00 functions_task.php
-rw-r--r--. 1 apache apache  23384 Mar 21 17:00 functions_time.php
-rw-r--r--. 1 apache apache  21600 Mar 25 20:04 functions_upload.php
-rw-r--r--. 1 apache apache  17338 Mar 21 17:00 functions_user.php
-rw-r--r--. 1 apache apache   2825 Mar 21 17:00 functions_warnings.php
-rw-r--r--. 1 apache apache     67 Mar 21 17:00 index.html
-rw-r--r--. 1 apache apache   8094 Mar 21 17:00 init.php
drwxr-xr-x. 3 apache apache   4096 Mar 25 20:05 languages
drwxr-xr-x. 2 apache apache   4096 Mar 25 20:05 mailhandlers
-rw-r--r--. 1 apache apache  17151 Mar 21 17:00 mybb_group.php
drwxr-xr-x. 2 apache apache   4096 Mar 25 20:05 plugins
-rwxrwxrwx. 1 apache apache      0 Jun 17 20:27 settings.php
drwxr-xr-x. 2 apache apache   4096 Mar 25 20:05 tasks

Yet only the config file and the cache directory are the ones that are complaining about not being properly modded. I have tried to do a fresh download and copy/paste the chmod commands from the documentation but that doesn't work. Changing the group/owner to root doesn't work. 

I must be missing something obvious here, any ideas?
looks like server has some weird cache ! check again after some time - may be an hour ..
(2016-06-18, 03:00 AM).m. Wrote: [ -> ]looks like server has some weird cache ! check again after some time - may be an hour ..

See the thing is, its my server (running CentOS7, standard LAMP stack). Restarting httpd or the server doesn't help :/
if you have ftp setup then can you check through a ftp client .. (also see if this has a clue)
(2016-06-18, 03:25 AM).m. Wrote: [ -> ]if you have ftp setup then can you check through a ftp client .. (also see if this has a clue)

Unfortunately that didn't help either. I eneded up just starting from fresh, it was easier than troubleshooting haha. Thanks anyways