This file, /var/www/html/admin/modules/blacklist/functions.inc.php, is causing freepbx to not write config files. When I run "/var/lib/asterisk/bin/retrieve_conf" this is what I get.
"Fatal error: Cannot instantiate non-existent class: ext_waitexten in /var/www/html/admin/modules/blacklist/functions.inc.php on line 66"
So just to see what would happen I changed the line from
$ext->add($id, $c, 'end', new ext_waitexten(60));
to
$ext->add($id, $c, 'end', new ext_wait(60));
then I get a different line number, 120, then after changing that one I get 91.
So after changing them all, config files are writing. I don't know if these are supposed to say wait instead of waitexten, but since I don't use the blacklist module yet, it solves my problem for now. If there is a better fix that will allow me to change these back, please let me know.