That would seem normal.
But, you said this all started happening around the time you were altering your configure.php and changing permissions, right?
Perhaps you've accidentally changed something else related to permissions.


Now, something that's puzzling ...
You said you renamed /includes/.htaccess to htaccess_off
When you did that, and then checked the server errorlogs, do you keep getting new permissions errors about /includes/.htaccess ?
You shouldn't.

So ... what happens if you delete the /includes/.htaccess file altogether? Don't rename it. Just delete it. That gets rid of the permissions issue which would follow the file when you rename it.