CentOS server, remotely hosted, but NOT on shared system, Moodle 2.8.5 (Build: 20150310) with a tinker course using default clean theme ... file system repo into which scp'd a ppsx and manually created a readme.txt file via editor.
The ONLY way I could get an error is by setting permissions on one file (the readme.txt file in example below) where the file was readable/writable/executabe for NO ONE.
[root@sos moodle28data]# cd repository/
[root@sos repository]# ls
[root@sos repository]# cd test
[root@sos test]# ls -l
-rw-r--r-- 1 root apache 12409780 Mar 16 14:51 module_10_slides.ppsx
---------- 1 root root 28 Mar 16 14:38 readme.txt
Then, and only then, did I see a 'frownie' icon with an X indicating Moodle could not see the file there.
Suggest changing the theme of a course using one of the file system repos you've shown in your screen shot to clean theme and see if the issue persist.
Might check your apache error logs to see if there is any complaint there.
Might also turn on debugging ... to see what Moodle might say.
'spirit of sharing', Ken