To the best of my knowledge, any config items that require input from admin into a dialog box means the data goes into the DB (ie, doesn't write to any files - thus no ownership/permission issues). If one changes the smtp server the change should be recorded in the DB.
select * from `mdl_config` where `name` like "%smtp%"
What could prevent that for happening? IF the db user in config.php of Moodle hasn't been granted all privileges.
http://dev.mysql.com/doc/refman/5.0/en/show-grants.html
It could be possible to set a table to read only, but moodle doesn't do that (I don't think!).
Cache? in browser, in server (APC or Zend Opcache or MUC).
Do you have any tool that would allow working directly with the DB? phpmyadmin or adminer addon in Moodle. In the above query of the DB of the mdl_config table for any plugin names that contain 'smtp' are the only records one need to add to get smtp to function.
This is beginning to sound like one needs to communicate with entities IT/Network department to see if there is not some filter/WAN protection thing running that might also fitler data.
'spirit of sharing', Ken