I am running org-mode 8.3.6 (8.3.6-6-g194e51-elpa
@ .../.emacs.d/elpa/org-20161003/) in GNU Emacs 24.3.1
(x86_64-pc-linux-gnu, GTK+ Version 3.10.7).

In this version, visibility cycling does not work as expected.  Consider
the following three-line example file:

* a
** b
** c

Consider the following sequence of commands:
1.  Place cursor on the letter b.  
2.  In the menu, choose Org > Refresh/Reload > Refresh setup current
buffer.
     (I do not know how to access this command directly).  
3.  Press TAB on your keyboard.  

If I do this in org-mode 8.3.6, my buffer looks as follows:

* a
** b
...

In this minimalistic example, pressing TAB once more will bring back the
line with the c, but in more complex examples, some parts of the buffer
seem to "get lost".  Moreover, I often find my files garbled like this
when I open them from the agenda. 

If I apply the above sequence of commands using my built-in org-mode
7.9.3, everything is fine.