Modules appear to install, but don't show up
We had this problem recently with a Centos server. If this is your scenario try 

# chcon -Rv --type=httpd_sys_content_t ./sites/all/modules

From man chcon change security context, recurse, verbose, type is web content.

Note. Probably a good idea to check what type the files that are working are first.

$ sudo ls --lcontext google_analytics/
-r--r--r--. 1 unconfined_u:object_r:httpd_sys_content_t:s0 apache apache 31504 Jan 15 14:41 googleanalytics.admin.inc